Frequently Asked Questions for Providers

1. What is NYSIIS?

NYSIIS is the acronym for the New York State Immunization Information System. NYSIIS is a free, web-based statewide immunization information system, also known as a registry, which maintains computerized immunization data of persons of all ages in a confidential and secure manner.

Article 21, Title 6, of Public Health Law 2168, was signed into law in August 2006. This law mandates the creation of a statewide immunization registry for New York State providers outside of the five boroughs of New York City for the purposes of collecting and storing mandated information on vaccinations administered to all persons less than 19 years of age.

2. Why is an immunization information system (IIS) needed?

A statewide immunization information system will serve as a repository to aid, coordinate, and promote cost-effective disease prevention and control efforts in New York State. By two years of age, more than 20 percent of the children in the U.S. have seen more than one health care provider. As a result, multiple medical records are created and parents often lack a complete and accurate record of their children's immunization status. An IIS acts as a connection between the multiple providers a family may have and keeps track of which immunizations have already been given, and which ones are needed. An IIS helps sustain high immunization rates and low disease levels with more efficient management of information. It will also save money by ensuring that children get only the vaccines they need and improve office efficiency by reducing the time needed to gather and review immunization records.

3. Do other states have immunization information systems?

Yes. Immunization information systems are operational in 46 states. The Centers for Disease Control and Prevention (CDC) has developed guidelines and requirements that will enable all states to exchange information. As of 2008, 75 percent of all children in the U.S. are enrolled in immunization information systems.

4. When will providers use NYSIIS?

The law mandates that as of January 1, 2008, all current immunizations administered to children less than 19 years of age, along with their histories, must be entered into NYSIIS within 14 days of administration.

5. Will immunizations given prior to January 1, 2008, to persons less than 19 years of age need to be reported?

Yes. All historical immunization information is required to be reported to NYSIIS for any patient less than 19 years of age receiving a vaccination after January 1, 2008. The law requires any health care provider who administers any vaccine to a person less than 19 years of age to report within fourteen days of administration, including "immunizations received by a person less than nineteen years of age in the past if not already reported."

6. Are provisions being made to defer start up by some providers until a later date?

Public Health Law Section 2168, which took effect January 1, 2008, specifies an "orderly implementation and operation of the registry." Regulations have been adopted to provide details to satisfy this requirement of the law. In order to assist providers with compliance, training occurs regionally across the State on an ongoing basis. T hose who are not currently participating are out of compliance with the legislative mandate and are behind in reporting. Failure to comply with public health law may result in monetary penalties.

7. The entry of data, including historical data, within 14 days, poses significant challenges for health care providers. Will there be any accommodations?

Implementing a statewide electronic system is a large undertaking. The New York State Department of Health (NYSDOH) recognizes that the initial entry of data within 14 days poses significant challenges for health care providers. DOH will rely mainly on training, technical assistance and other supports for physicians and their staff to implement the system.

To assist providers with building the historical database, several activities are already underway including:

  • Obtaining and uploading vital record birth certificate information, including the hepatitis B immunization administered at birth, for children who were born in New York State outside of New York City after January 1, 2004; and
  • Encouraging and facilitating historical downloads from provider electronic data systems.
  • Providing training on the most efficient way to enter historical information.

8. What immunization data elements are required to be reported to NYSIIS?

Information required to be reported for immunizations administered after January 1, 2008 includes:

  • Patient's name, date of birth, gender, and complete address, including county of residence;
  • Mother's maiden name; and
  • Vaccine administration date, type, lot number and manufacturer.

Note that many of the variables listed above will be pre-populated as part of the vital records birth certificate feed for children born after January 1, 2004.

Additional data fields are available in the NYSIIS application to collect information that the provider may find useful.

9. What if a provider's historical records do not contain all of the data elements available in NYSIIS?

Some provider's existing records of historical immunization information contain most, but not all, of the required data fields. For example, providers may not have mother's maiden name, vaccine lot numbers, or manufacturer for historical immunizations. In these instances, reporting of all available historical information should occur when all of the required data fields are submitted for the current immunization. Incomplete information for immunizations administered prior to January 1, 2008 will be accepted. If missing information is not available to the provider, the Department may ask the provider to attest to this fact as part of future quality assurance activities.

10. Can NYSIIS help a provider's practice with Vaccine for Children (VFC) Reporting?

Yes. Once an organization actively begins reporting immunizations to NYSIIS, VFC tracking Reports, such as Doses Administered, can be generated and utilized to meet reporting requirements. However, to have NYSIIS generate this information, it is imperative that all patient data reported to NYSIIS is complete and accurate. This includes not only the vaccine information (i.e., lot number and manufacturer), but also the VFC eligibility status. It is the provider's responsibility to review these reports to ensure VFC eligibility is being recorded appropriately.

11. What are the benefits of NYSIIS to a provider's practice?

NYSIIS offers many benefits to providers. NYSIIS will:

  • Provide record consolidation of immunization information from multiple providers into a single reliable record. This record can then be used to provide official immunization records for school, licensed day care center, and camp entry requirements;
  • Aid in managing immunizations so that children receive only the vaccines they need within the appropriate timeframes;
  • Clarify complex and changing immunization schedules and emerging vaccine combinations;
  • Allow providers' offices with electronic medical systems to submit data without duplicate entry;
  • Generate reminder and recall postcards and/or mailing labels to send out to parents to remind them when their child's immunizations are due or have been missed;
  • Decrease time spent by office staff seeking immunization histories from previous providers;
  • Assist in the management of vaccine supply and ordering;
  • Generate timely immunization reports to assist with Vaccines for Children (VFC) reporting requirements; and
  • Assist in preparing HEDIS and QARR reports and other quality improvement initiatives.

As a result of these immediate benefits, providers will realize many long-term benefits such as a reduction in paperwork, staff time and costs associated with immunization related activities.

12. How will NYSIIS affect my office staff's busy workload?

Depending on a provider's current office system, there may need to be an increase in staff efforts devoted to data entry of existing patient information into NYSIIS. However, once the initial investment of staff time to enter immunization histories is completed, NYSIIS will actually reduce the staff time required to:

  • Search for or replace medical records;
  • Provide immunization records for school, camp, or other activities;
  • Calculate which vaccines are due;
  • Give unnecessary immunizations when earlier immunization records are missing;
  • Request immunization records from other providers; and
  • Track vaccine inventory.

13. What are the minimum requirements for the computer equipment and software needed to access NYSIIS?

To receive the full benefit of NYSIIS, a provider will need to have a computer with reliable public internet access, preferably with a dedicated, high speed connection. The following are minimum hardware and software requirements to access NYSIIS:


  • Pentium 500 MHz computer or higher
  • 64 MB RAM or greater
  • 500 MB free disk space or greater
  • Screen display set at 800 x 600, 256 colors; 1024x768


  • Internet Browser Software –
    • Microsoft Internet Explorer 7.0 or higher
  • Microsoft Windows 98 or higher
  • Adobe Reader 6 or higher

For networked computers, port 543 of the network firewall must be open for outgoing HTTPS.

14. Are fees associated with participation in NYSIIS?

There is no fee for the use of NYSIIS. The only cost that may be incurred is associated with maintaining internet access.

15. How will providers access NYSIIS?

Users will access NYSIIS through the NYSDOH Health Commerce System (HCS). All NYSIIS users are required to have an individual HCS user account. Medical professionals can apply online at at any time. A medical professional who signs up may designate another user to be the HCS Coordinator for his or her practice. The HCS Coordinator obtains and manages the medical practice user accounts (for medical and non-medical staff) on the HCS and is the principal point of contact concerning HCS access. It is recommended that offices designate at least two HCS coordinators.

Obtaining an HCS account offers medical professionals many advantages including the ability to receive important NYSDOH communications and notices, access the Health Alert Network (HAN), enroll in the Health Department's Public Health Preparedness Practitioner Volunteer Program, receive disease information, and participate in other educational opportunities. In addition, medical professionals who are licensed to prescribe also have the ability to order official New York State prescriptions online, customize the official prescriptions, and access the Physician Profile.

16. Can medical office staff enter records into NYSIIS?

Yes. Though the provider has the responsibility for the submission of immunization records according to the requirements of the legislation, he or she may authorize additional members of the office staff to enter the records.

17. How can records be submitted to NYSIIS?

Providers will be able to submit records either:

  • Through a secure internet site –on the NYSDOH Health Commerce System.
  • By direct interface with their medical billing or clinical management software. This will require the medical software vendor to create an interface program to meet NYSIIS specifications.

18. Does NYSIIS integrate with an existing computer system? What if I already have immunization information entered into my own computer system?

NYSIIS can be used successfully in practices both with and without electronic medical record and billing systems. In an attempt to minimize the amount of manual data entry into NYSIIS, the new web application does comply with HL7 standards and does have ASCII flat file upload capabilities. Specifications have been developed to allow software vendors to create an export file from clinical record or billing systems for

NYSIIS. Each system will need to be tested to see if the export file meets the NYSIIS requirements. For electronic transfer specifications and additional information on getting started with data exchange, go to the following website: .

19. Are patients' records in NYSIIS kept secure?

Through built-in system security features, only providers and authorized users will be able to directly access a patient record. When searching for an individual record, providers will not be able to view more than a limited number of records while attempting to identify their unique patient. Search criteria for an individual patient will require specific and accurate information and search results will yield a limited number of matches in order to further protect confidentiality.

Parents or guardians may obtain a child's immunization record from their provider, public health department or by requesting the record from the NYSDOH Bureau of Immunization.

Each user of the system will be required to have an individual HCS user account and password. Users sign the Security and Use Policy when obtaining an HCS account. In addition, users sign a NYSIIS user agreement at the time of training. Both the security policy and user agreement ensure a user acknowledges they understand that the information in NYSIIS is confidential and that they will be penalized if they violate that confidentiality or in any way abuse the information to which they have access. All access to the system and every transaction will be recorded and such records will be reviewed and audited.

Breaches of confidentiality, regardless of the nature, are subject to medical confidentiality laws as specified in the Public Health Laws.

20. Are the data collected for NYSIIS subject to provisions in the Health Insurance Portability and Accountability Act (HIPAA) of 1996?

NYSIIS is exempt from the HIPAA Privacy Rule. Under HIPAA, covered entities are permitted to report information to public health authorities and HIPAA does not supersede state law in this respect.

21. How will the accuracy of NYSIIS data be validated?

When data are submitted, comprehensive edit checks and de-duplication processes are executed to validate the data being submitted. In addition, data are evaluated for completeness, timeliness and accuracy on a regular basis. In some instances, it may be necessary to verify the information with the submitter.

22. Will the New York City immunization registry, the Citywide Immunization Registry (CIR), and NYSIIS be joined together?

No, both registries will continue to operate independently. The public health law allows records to be shared between the two registries. Currently, there is a one way transfer of patient records from NYCIR to NYSIIS. NYSIIS only receives records from NYCIR for patients whose documented address is outside the 5 boroughs.

23. If a provider has a practice in New York State, outside of New York City, but their patient's address is in New York City, how should they report?

An immunization is reported to only one registry based on where the immunization is administered. An immunization administered by a provider in New York State, outside of New York City, would be reported to NYSIIS regardless of where the patient resides. Likewise for providers in New York City, they will continue to report to the CIR.

24. Can the immunizations given to an adult be reported?

Immunizations administered to individuals 19 years of age or older may be included in NYSIIS with the consent of the vaccinee. A consent form for this population has been developed for NYSIIS.

25. What happens to a person's records when they reach 19 years of age?

Their record of immunizations received prior to 19 years of age will be maintained in NYSIIS. However, any immunizations received after turning 19 years will only be added to NYSIIS if consent is documented in NYSIIS.

26. How do parents/guardians obtain copies of their child's immunization record?

For records from NYSIIS for children less than the age of 19 years, parents/guardians must request copies from their primary care provider or the local health department or by requesting the record from the NYSDOH Bureau of Immunization.

27. Will children with medical or religious exemptions need to be included in NYSIIS?

These children will be entered in NYSIIS and their records noted with the appropriate exemption. NYSIIS is a valuable tool to identify and protect these children in the event of an outbreak of a vaccine preventable disease.

28. Will parents/guardians receive notification of their child's inclusion in NYSIIS?

Yes. NYSDOH has developed a one page document that providers will use to notify parents/guardians of newborn or newly enrolled children, including where to obtain additional information. This notification is available for download from NYSIIS. Providers must notify parents at the time of administration of the first immunization that the child's immunization information will be included in NYSIIS going forward.

29. Who will have access to NYSIIS?

The following is a list of "Authorized users" as defined in PHL 2168 and the level of access granted:

Full Access:

  • New York State Department of Health
  • Local health departments
  • Health care providers and their designees
  • Hospitals
  • Office of Children and Family Services
  • Certified Home Health Agencies

Read Only Access:

  • New York City Department of Health and Mental Hygiene
  • Educational institutions* (schools K-12, day care centers, Head Start Programs, colleges and universities)
  • Local Social Services *
  • WIC agencies
  • Other state and local health departments outside of New York

Query Only Access:

  • Health Insurance Plans and other third party insurers (perform quality assurance activities, accountability, and outreach pertaining only to their plan enrollees).

* Read only access unless they administer immunizations.

30. Where can I obtain additional information if I have further questions?