NYSIIS Initial Setup

The New York State Immunization Information System (NYSIIS) is the web-based statewide immunization information system for New York State providers outside of the five boroughs of New York City.

NYSIIS was developed as required under Article 21, Title 6, Section 2168 of the Public Health Law. This law, which took effect January 1, 2008, mandates health care providers to report all immunizations administered to persons less than 19 years of age to the New York State Department of Health (NYSDOH). The law also requires that immunization histories of all persons less than 19 years of age who receive vaccines after January 1, 2008 also be recorded in NYSIIS, if those histories have not already been reported.

The Public Health Law provided a two year implementation period to enable providers to be phased in through continuous regional roll out. Since 2008 multiple training opportunities and methods have been available to all providers statewide. It is important to note that those who are not currently participating are out of compliance with the legislative mandate. Failure to comply with public health law may result in monetary penalties. It is imperative that any provider organization that has not yet taken training or begun reporting to NYSIIS take the necessary steps to do so.

The following information is included in this letter:

  1. Health Commerce System (HCS) Account Instructions
  2. NYSIIS User Roles
  3. Training Options
  4. Pre and Post Training Checklist
  5. Where to Get Additional Information

1. Health Commerce System (HCS) Account Instructions

The NYSDOH Health Commerce System is a secure intranet designed by NYSDOH specifically for electronically exchanging health related data and information between health care providers and NYSDOH.

Individual HCS accounts are required for accessing NYSIIS. All NYSIIS users should have their own personal active HCS account prior to training. HCS accounts cannot be shared. Without an HCS account, users will not be able to access the NYSIIS application.

  • A prescribing medical professional within a practice can request an HCS account at the following Department of Health web site: Health Commerce System (HCS)
  • Any prescribing medical professional who obtains an HCS account is automatically given "Director" and "HCS Coordinator" roles.
    • The HCS Coordinator role is authorized to manage the medical practice user accounts on the HCS and be the principal point of contact concerning HCS access. The Coordinator will be given access to approve user account requests for other staff, which include non-medical office staff. This can be done by following Step B located here: New HCS User Account (PDF)
  • The prescribing medical professional may delegate the Coordinator role to one or more medical or non-medical staff members. It is recommended that an office designate at least two staff as Coordinators. Every HCS Coordinator must have an active HCS account. This can be done through the Health Commerce web site by logging on: Health Commerce System (HCS) and accessing Coord Account Tools- HCS and requesting a "Coordinator" account.
  • All staff from providers' practices that will be responsible for accessing NYSIIS will need HCS accounts. Each user needs to have their own PERSONAL, unique login id and password.
  • Users can apply for an account by following the instructions in Step A located here: New HCS User Account (PDF)

If you are not sure if your work site has previously applied for access to the HCS, or who your HCS Coordinator is, you can contact the Commerce Account Management Unit (CAMU) Help Desk at 1-866-529-1890 or hinhpn@health.ny.gov.

CAMU Hours of Operation for account information and passwords - 8AM-4:45PM EST excluding weekends and closed holidays.

2. NYSIIS User Roles

NYSIIS is set up to accommodate a variety of user types. Each user will have access to certain features of the application based on the role assigned to them. Training opportunities targeting both the NYSIIS Administrative User and the NYSIIS Standard User roles are available.

  • NYSIIS Administrative User - This is the main contact for NYSIIS within the health care organization. The administrative user can access all features of the application. Only the administrative user will be authorized to provide access to NYSIIS for all appropriate staff by adding them as NYSIIS users to the system. Other responsibilities include maintaining all organization specific information and adding and maintaining physician and school information for their organization. In addition, if your organization chooses to utilize the vaccine inventory functions available within NYSIIS, only the Administrative User will have access to add and manage vaccine inventory. If your organization participates with the NYSDOH Vaccine Program, then the administrative user will have access to the vaccine ordering module as well.
    Please Note: Administrative Users must receive both Standard User and Administrative User training.
  • NYSIIS Standard User - This is the most common user role for NYSIIS. The standard user adds, edits, and finds patients, manages immunization information, and can run and print various immunization reports (e.x., Patient Specific, Doses Administered, Reminder Recall, etc.). This type of user should seek NYSIIS Standard User training.

3. Training Options

For participants to receive the maximum benefit of training and to ensure training remains focused on the training-related content, training participants are expected to have the following basic knowledge:

  • General computer skills necessary to operate and navigate Windows based applications.
  • Computer related terminology and acronyms (e.g., icon, desktop, search, toolbars, menus).
  • Use of the internet, including accessing, navigating and using search engines (browsers).
  • General knowledge of immunizations.
  • General knowledge of their organizational processes and procedures, particularly for those users who will be functioning as a NYSIIS Administrative User.

Primary Training Options:

All NYSIIS training is accessed through the NYS Public Health Learning Management System (LMS)

To learn how to obtain a LMS account, enroll in courses and view our NYSIIS post training instructions, please follow this link to the NYSIIS Training Page.

Supplemental Training:

The NYSIIS User Manual can be used in conjunction with the NYSIIS LMS training courses. The user manual is not intended to be the sole source of training for new users.The NYSIIS User Manual is available online on our NYSIIS Training Page and can be accessed by clicking the training page link above.

Webinar Training:

The NYSIIS LMS courses are set up as prerecorded webinars. A webinar provides demonstration of the NYSIIS application via the internet. It is a convenient training format that allows participants to watch training from their office computer. User trainings are available for viewing at any time that is convenient. Other recorded webinars regarding NYSIIS specific functions are available on the LMS as well.

Live "Ask the Trainer" webinars are offered monthly. During the live webinar sessions, participants will be able to communicate with the webinar trainer. "Ask the Trainer" webinars are open forum sessions where participants can ask specific questions. The trainer can provide a demonstration of the NYSIIS functions related to user questions.

4. Pre and Post Training Checklist

The following list is provided to assist you with tracking the activities to be completed before and after training.

Before NYSIIS Training:

  • Ensure all staff have their own HCS Account.
  • Verify HCS Account is active by successfully logging into the HCS home page at: Health Commerce System (HCS)
  • Assign NYSIIS user roles for your office:
    • Administrative User
    • Standard User
  • Have staff set up a LMS account and view required training.

After NYSIIS Training:

  • Complete NYSIIS User Agreement for each staff member accessing NYSIIS
  • NYSIIS Administrative User adds all other NYSIIS users to the system.
  • Training participant disseminates NYSIIS information and provides training for other office staff.
  • Begin reporting to NYSIIS.
  • Begin distributing NYSIIS parental notification when immunizations are administered.

5. Where to Get Additional Information

For more details on the legislation and NYSIIS, please visit our website:

We are very appreciative of your support for this important public health activity. Your participation is invaluable to the program's success. You may also contact NYSIIS staff at (518) 473-2839 or email NYSIIS@health.ny.gov with additional questions.