When you start giving immunizations in your office, you will need to document immunizations in your EMR, even if you also have to record in a provincial system.

Given how new COVID-19 immunizations are, your EMR might or might not have specific documentation best practices, so you will have to decide for yourself how to adapt.

EMR specific EMR-Specific recommendations and features are described below for several EMR products. If your EMR is not listed there, please approach your EMR support.

As a team, you will have to decide which approach or approaches will work best for your group and use it consistently.

NOTE: Some of this information is for the person who might be actively making the changes in your EMR (and only needs to be done once).

Custom Options and Goals

You want to record immunizations in your own EMR for a few reasons:

  • recall for second dose (with correct vaccine) and not calling people unnecessarily who have had the vaccine
  • follow up in case of side effects
  • for your patient record
  • for billing

There are several places you can choose to record in your EMR from free text somewhere (i.e. note) to the specific immunization section and potentially a few places in between. Several common approaches are described next.

We recommend you use your immunization section in your EMR for documenting COVID-19 immunizations. You may also want to use one of these additional options as well for improved workflow or for generating recall lists.

Immunization Section


  • This is where immunizations are meant to be recorded – your EMR is built for this.
  • You can document additional details such as lot number, injection site, etc.
  • The coding system is clear and EMRs, if they are connecting out to other systems (e.g. for eReferrals), would share the immunizations correctly.
  • If you want to search or query those who are immunized in the future, documentation in the ideal place will mean the data is retrievable.


  • Many primary care offices do not consistently use the immunization module, so for some, this might be an unfamiliar area of your EMR.


Look to your EMR vendor’s website to see if they have already updated their EMR with the codes or vaccine names.

If you need to manually add the COVID-19 vaccine produces into your own EMR, most EMRs will let you add and you can put in specific information.


If you are adding new vaccines, we recommend you use the “AIG” (Active Ingredient Group) code if that is an option (see the table below). We have included the “DIN” (Drug Identification Number) and the ATC codes in case those are your only options. In general, the DIN is more specific than you need and the ATC code is too general (all COVID-19 vaccines fall under J07BX OTHER VIRAL VACCINES).

When using your EMR in your visit, you will need to add the vaccine given in the immunization or vaccine section or however you do that in your EMR.

VACCINEAIG CodeDIN Code (example)ATC CodeDoses
ASTRAZENECA COVID-19 VACCINE016272200102510847J07BX2
JANSSEN COVID-19 VACCINE016278800102513153J07BX1
COVID-19 VACCINE MODERNA016266200102510014J07BX2
Current list of approved COVID-19 vaccines in Canada and their corresponding codes.

Document on the Problem List


  • Many of us are used to putting issues on the problem list. They are often easier to see in the chart and can be structured / coded and even commented on.
  • Many practices use the problem list already to generate recall lists (e.g. for diabetes, CHF, etc.) so your office probably can create a recall list using the problem list.


  • Usually the code system in Canadian Primary Care EMRs is ICD9. ICD9 was not made for vaccines, so you have to hack in using a code that is close and relabel it for readability.
  • Your problem list will quickly get cluttered – initially it makes sense but as 70+% of patients are immunized, most people will have 1-2 extra “problems” for their immunizations.


In your EMR you need to add several diagnoses to the diagnosis table (each EMR has different terms). Most EMRs use ICD-9 codes and there is NOT an agreed to ICD-9 code for COVID-19 or COVID-19 immunization (some provinces have made custom codes (e.g. BC has C19 for the diagnosis but this is NOT for the vaccine). Label each diagnoses distinctly by vaccine type.

Add to patients problem list when you administer or confirm they have had an immunization.

Use a COVID Immunization Visit Template


  • You can design a focused immunization template that also covers off items like:
    • History – contraindications screening
    • Consent
    • Last dose / next dose
  • This will help with the documentation needs for COVID immunization visits, ensuring consistency.
  • You can, in some EMRs, include billing into your visit template to speed things up.
  • You may find one already built by your EMR or in your EMR community form library that you can use.


  • It may take a bit more time to set up.
  • Requirements for documentation may shift.
  • You still need to figure our how to code the immunization as some EMR template tools do not include coded information that can be searched.
  • The biggest con is that it is just for immunizations given in your office and you cannot use it for recording immunization status (e.g. given at another clinic, hospital, etc.).


Look to your EMR instructions on how to create a visit template, custom form, eForm or the like.

Add an Encounter Diagnosis


  • Many of us are use to using codes in the encounter or visit diagnosis section of our EMR visit note, so this can be added easily into our workflow.
  • They are date stamped at the visit, so easier to track when it was given.
  • Often links to billing module, speeding up your workflow.


  • Uses the same codes as the problem list, and these ICD-9 codes were not made for immunizations, so you have to hack it in using a code that is close and relabel it for readability.
  • Over time, in patients with lots of visits, the immunization visit gets buried in the visit list.
  • This is better used to document when you give an immunization vs status of immunization.


See how to add to your diagnosis table in the Problem List section.

Add to visit diagnosis (impression, assessment, etc.) at the visit.

Use Billing Codes


  • Many provinces are adding specific billing codes for COVID-19 immunizations. In some provinces, billing is linked to provincial immunization registries, so doing this consistently is an absolute requirement.
  • Many offices will be documenting this regardless in order to be paid.
  • Generally, offices know how to run searches based on billing codes, if you are running fee-for-service.


  • Billing is meant for activities in the office, so it is not good if you want to consistently document who in the office is immunized, independent of where they received it.
  • Billing codes may not be useful if a different team member provided the immunization.
  • Billings may not be used in alternate funding models – other tracking is needed.
  • Billing codes will not likely distinguish the type of vaccine administered so in the case of recall or re-administration requirement based on lot number this information will not be enough.


Look to your provincial fee code system to determine the code.

Consistently bill this for your immunizations.

Write it as a Prescription

We do not recommend you do this unless you also need to prescribe it so it can be dispensed (which you do not for COVID-19 immunizations at this time).

Write it in Free Text (somewhere in the chart)


  • This is the simplest approach. The biggest PRO here is that we all can do this and you can start right away.


  • All you have is an electronic paper record. This is not the recommended approach. While you have documented it, that is all you have done. You cannot really use any tools in your EMR to recall patients, find out how many patients have or have not had their immunizations etc.
  • Typos are a huge problem, because you might record that you gave Pzifer, or Medorna, or AZ, AstraZ, AstrZinica, J&J, JandJ, JJ… you get the picture.


Just start typing… but we do not recommend this as your only approach.

EMR-Specific Recommendations and Features


EMR-specific tools and resources have been identified and outlined by OntarioMD here:

Accuro QHR

EMR-specific tools and resources have been identified and outlined by OntarioMD here:

Arya EHR

Arya EHR has a vaccine module that allows practitioners to record all the details of vaccine administration (including Covid) and also create/track tasks for callbacks for second doses or boosters. With our callbacks we have automatic reminders that go out to reduce the administrative burden of confirming these patients. We also offer patient self online booking to make it easy to book a vaccine appointment or otherwise! We have a full suite of virtual tools with our EHR in addition to the usual features including e-prescribing, online booking, telehealth and more.

Avaros EMR

Avaros has a prevention module where Providers can record preventative therapies, including immunizations, and receive reminders when certain preventions are due. In the case of the Covid-19 vaccine, all patients have been flagged as requiring 2 doses of the vaccine if they are > 16 years old. Reminders are active for all patients meeting that criteria unless 2 doses have been recorded in the EMR, in which case the vaccination is listed as completed.

Healthquest/Microquest EMR

As per the December 7, 2020 announcement:

“Alberta Health has asked health practitioners to report immunizations via the Immunization Direct Submission Mechanism (IDSM). For more information on how to access the IDSM, visit https://www.albertanetcare.ca/learningcentre/IDSMAccess.htm … a [direct] immunization submission feature is not feasible at this time … If you have any questions, do not hesitate to contact Microquest. “

IntraHealth (Profile) EMR

IntraHealth has developed its own COVID Toolkit for customers. The toolkit can be accessed through the learning hub here:
IntraHealth Customer Learning Hub Marketplace
The toolkit can be found under the category: ‘Other download’ for any province. The .zip file will contain all the files to import into Profile EMR, along with an instruction sheet.

Juno EMR

Juno EMR has added a prevention within patients eCharts for tracking COVID-19 vaccines. Custom reports would then be run to determine which patients have received 1st/2nd dose, the vaccine provided, date of shot, dosage and lot#. These custom reports are then provided either as plain-text display in a table, or exported directly to Excel on the physician’s computer. The preventions section within Juno EMR will be largely the same as other OSCAR EMR service providers.

The OSCAR User’s society has a guide on adding and managing these preventions found here: OSCAR Manual on Preventions


LibreMD does not have any specific reporting guidelines at this moment, but is providing their customers with custom queries free of charge, as the need arises.


MOIS EMR has tools and guidelines designed to help users document and identify populations vulnerable to COVID-19. This allows providers to generate reports so that they could potentially reach out to patients and make sure they get scheduled for vaccination or confirm their vaccination. Canadian-approved vaccine details are also added to their system as they are approved. Customers routinely receive updates and announcements regarding resources available in MOIS EMR. For a copy of their latest documentation guidelines, please visit their resources page for customers here:
Bright Health Customer Resources


MYLE EMR recommends following the “Updating a Patient’s Medical Summary” guide found here:
MYLE EMR’s Guide on Updating a Patient’s Medical Summary

Ofys EMR

There are two ways to record immunizations in Ofys. One is simply noting it in the visit, and it updates automatically the patient summary. The other is linked directly to the patient’s INSPQ vaccination profile. The clinician can see the patient’s profile and add the new immunization there directly.


Currently in OSCAR users can record the COVID-19 vaccine under the “Preventions” module of the eChart to indicate that the patient received the vaccine and details around that. They can enter both dose’s as well by adding another entry at a later date. There is also a preventions report in OSCAR already where they can report on the number of patients with the vaccine captured if they choose to.

The OSCAR User’s society has a guide on adding and managing these preventions found here: OSCAR Manual on Preventions

EMR-specific tools and resources have been identified and outlined by OntarioMD here:

Telus PS Suite

EMR-specific tools and resources have been identified and outlined by OntarioMD here:

Scroll to Top