Background: A severe influenza vaccine supply shortage occurred in the 2004-5 influenza season. Did this shortage change the factors associated with influenza vaccination for seniors in San Diego County? Methods: Two consecutive years of cross-sectional survey data collected by the County of San Diego, the random digit dialing surveys (RDDs) of 2004 and 2005, were analyzed for the respective 2003-4 and 2004-5 influenza seasons to identify factors related to influenza vaccination of seniors. Multivariate logistic regression was used to assess factors related to the outcome of current influenza vaccination for each year. Associated factors were noted and compared. Results: This study found that the group-level factors related to senior influenza vaccination in 2003-4 influenza season were almost identical to group factors in 2004-5 season. The factors that were related for both years were (1) Participant belief of belonging in a group that should be immunized for influenza or pneumonia, and (2) Having ever received a pneumococcal vaccination. In 2003-4, highest level of education was identified as a confounder, but in the 2004-5 season this factor did not sustain as a confounder for a severe vaccine shortage year. Conclusions: Vaccination of seniors during a vaccine supply shortage occurred regardless of highest level of education attended. Seniors may have accessed the influenza vaccine differently, providers may have changed their vaccination practice to accommodate priority groups, or the approaches used by the County of San Diego to vaccinate priority groups in response to the vaccine supply shortage were successful. Compared to all seniors for each respective year, seniors who self-identified as being high-risk had the highest influenza vaccination coverage rate. For the 2005 survey, seniors who self-identified as being affected by the vaccine shortage had a lower vaccination rate than all seniors. Missed vaccination and additional vaccination education opportunities were identified as a small number of seniors received the live, attentuated influenza vaccine over the recommended trivalent inactivated vaccine.