BACKGROUND: As the number of providers administering vaccines increases, including pharmacists, there is a concern of fragmented immunization records in state and regional immunization information systems (IIS). In order for IIS to have complete records, it is critical that each provider administering vaccines, including pharmacists, participate and update the IIS each time a vaccine is administered to a patient. In Alabama, provider participation in the state IIS is not mandatory; as a result, less than 25% of adults over the age of 19 have immunization data recorded. IIS participation among independent pharmacies is of particular concern as approximately 40% of Alabama pharmacies are independently owned, but only 27% of these are enrolled in the IIS. OBJECTIVE: The objective of this report is to describe a study protocol to assess the impact of an IIS training program among community pharmacies' IIS enrollment and actual participation rates. METHODS: The research design is a randomized controlled trial. Study participants are Alabama pharmacists who work in independently owned pharmacies that currently provide at least one type of non-seasonal vaccine and are not currently enrolled in the Alabama IIS. Multiple outcomes including awareness, knowledge, attitudes, intention, IIS enrollment, and IIS participation will be compared between intervention and control groups across three time points (baseline, one-month, and three-months). Individual and organizational factors will be measured to identify any possible associations with outcomes. IMPLICATIONS: The expected outcome is to create an effective training program that is scalable and ready for dissemination. If successful, this training program can be replicated and used to significantly impact the completeness and accuracy of IIS across the U.S., providing the potential for IIS to be used consistently in assessing immunization status and recommending additional vaccines in the pharmacy setting, thereby improving vaccination coverage and making the provision of immunizations safe and efficient.