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Immunization Records in Practice Fusion: Keeping Track of COVID-19 Vaccinations

With the rollout of the COVID-19 vaccines, it has never been more important for clinicians to keep track of their patients’ immunizations. Vaccine guidelines require medical professionals administering vaccines to record vaccine information:

  • On their patients’ vaccine “cards” immediately1,2
  • In their own record-keeping system within 24 hours3,4
  • By reporting to the state vaccine registry as soon as practical and within 72 hours of vaccine administration.3,4

In this article, we look at the reasons it is important to track vaccine administration. We also share how the Practice Fusion electronic health record (EHR) system can help you track both the vaccines you’ve given out and the vaccine doses remaining in your inventory.

Why Is it Important to Track Vaccinations?

Three different COVID-19 vaccinations are currently being given: one manufactured by Pfizer-BioNTech and one by ModernaTX that each require two doses, and one by Janssen (Johnson & Johnson) that requires only one dose. It’s of key importance to record which type of vaccine a patient receives, as each patient must receive the same type of vaccine for both their first and second dose. In addition, the record must note when the second dose is due because the second dose must be given a specific length of time after the first for maximum effectiveness. For the Pfizer-BioNTech COVID-19 vaccine, the two doses are separated by 21 days; for the ModernaTX COVID-19 vaccine, the two doses are separated by 28 days.3,5,6

Vaccine kits contain a card on which to record the patient’s name, vaccine manufacturer, and due date for the second vaccine dose. Physicians can track their patients’ immunizations electronically by recording an immunization in the Practice Fusion EHR.1,2

While the federal government is currently paying for the COVID-19 vaccine, it is also important to track vaccinations for billing and inventory purposes.7,8 The vaccine will be free to the public under the Coronavirus Aid, Relief, and Economic Security (CARES) Act and the uninsured will be vaccinated for free.8,9 Private insurers and Medicaid programs will cover the cost of the vaccine so there is no charge to the individuals.7

State-by-State Mandates for Reporting

Each state has its own unique mandates for reporting vaccination information so please check the reporting mandates for your specific state.

Practice Fusion helps providers integrate electronically with supported state immunization registries. To set up an integration with your state immunization registry, first confirm that your state registry is listed in the Practice Fusion Supported Immunization Registries table found in this Knowledge Base article. If it is not listed on the table, your state is most likely not yet ready to receive immunization data electronically. Please contact your local registry for more information.6

Once you have confirmed that your state registry is ready to receive immunization data electronically, register with your state immunization registry.

1. Connect Practice Fusion to your state registry.
2. Register each facility in your practice.

3. Enter Production and Testing information. If you do not know any of the information required in this section, make sure to contact your local registry.
4. Send test files to validate the process.
5. Activate your immunization integration in the Immunization registry settings page.
6. Submit immunization records directly to your local registry.
For instructions on adding a vaccine, see: How do I record a vaccination to transmit successfully to my immunization registry?

Immunization Records in Practice Fusion

The Pfizer-BioNTech, ModernaTX , and Janssen (Johnson & Johnson) COVID-19 immunizations and CPT codes are currently available in the Practice Fusion EHR. Information for other COVID-19 vaccinations will be added to the EHR as they receive Emergency Use Authorization.2 CPT codes can be used to record the procedure on a patient’s chart. For billing purposes, they can also be used to create documentation for payers.

In addition to COVID-19 vaccines, Practice Fusion can also help you track other routine immunizations, such as influenza.

In order to transmit a patient’s immunization record to the state immunization registry successfully, the patient’s administered vaccines 1) must be entered, and 2) must contain all the required information:

  1. Enter protection indicator instructions.
  2. Access patient’s immunization section.
  3. Add vaccine.
  4. Fill in required details.
  5. Transmit.

If you have questions about how to record a patient’s vaccination so it will transmit successfully to your state immunization registry, see: How do I record a vaccination to transmit successfully to my immunization registry?

Tracking COVID-19 vaccines is required by the United States government.3,4 It is also a useful method of tracking patients’ immunization status when they have received only one of the two doses, and for tracking your inventory of vaccines. Practice Fusion can help you connect to your state registry if your state registry is set up to receive immunization data electronically.

Regardless of whether your EHR can communicate with the state immunization registry, Practice Fusion can help you to track the immunizations you’ve administered as well as your remaining inventory of vaccines.


  1. Bonifield J, Vera A. Vaccination cards will be issued to everyone getting Covid-19 vaccine, health officials say. Updated December 3, 2020. Accessed February 17, 2021,
  2. Pugle M. You’ll Get a Vaccination Card with Your COVID-19 Vaccine: Why It’s Important. Healthline. Updated December 12, 2020. Accessed February 17, 2021,
  3. Centers for Disease Control and Prevention (CDC). Pfizer-BioNTech COVID-19 Vaccine. CDC. Updated February 16, 2021. Accessed February 17, 2021,
  4. TOOLKIT ON COVID-19 VACCINE: HEALTH INSURANCE ISSUERS AND MEDICARE ADVANTAGE PLANS. 2021. January 7, 2021. Accessed February 18, 2021. - files - document - COVID-19-toolkit-issuers-MA-plans.pdf
  5. Centers for Disease Control and Prevention (CDC). Information about the Moderna COVID-19 Vaccine. CDC. Updated January 25, 2021. Accessed February 17, 2021, - coronavirus - 2019-ncov - vaccines - different-vaccines - Moderna.html
  6. Weise E. When there’s a coronavirus vaccine, how will we make sure everybody gets it? That’s the job of state immunization registries. USA Today. Updated June 13, 2020. Accessed February 17, 2021,
  7. COVID-19. Centers for Medicare & Medicaid Services (CMS). Updated January 19, 2021. Accessed February 18, 2021,
  8. Gerencher K. Will the COVID-19 Vaccine Be Free? Good Rx. Updated December 14, 2020. Accessed February 17, 2021,
  9. Ries J. You Won’t Have to Pay for a COVID-19 Vaccine, At Least in the Beginning. Healthline. Updated December 10, 2020. Accessed February 17, 2021,