Background Only a small amount of research has focused on the relationship between socio-economic status (SES) and geographic access to prescription medications at community pharmacies in North America and Europe. To examine the relationship between a community’s socio-economic context and its residents’ geographic access to common medications in pharmacies, we hypothesized that differences are present in access to pharmacies across communities with different socio-economic environments, and in availability of commonly prescribed medications within pharmacies located in communities with different socio-economic status. Methods We visited 408 pharmacies located in 168 socio-economically diverse communities to assess the availability of commonly prescribed medications. We collected the following information at each pharmacy visited: hours of operation, pharmacy type, in-store medication availability, and the cash price of the 13 most commonly prescribed medications. We calculated descriptive statistics for the sample and fitted a series of hierarchical linear models to test our hypothesis that the in-stock availability of medications differs by the socio-economic conditions of the community. This was accomplished by modeling medication availability in pharmacies on the socio-economic factors operating at the community level in a socio-economically devise urban area. Results Pharmacies in poor communities had significantly higher odds of medications being out of stock, OR=1.24, 95% CI [1.02, 1.52]. There was also a significant difference in density of smaller, independent pharmacies with very limited stock and hours of operation, and larger, chain pharmacies in poor communities as compared to the middle and low-poverty communities. Conclusions The findings suggest that geographic access to a neighborhood pharmacy, the type of pharmacy, and availability of commonly prescribed medications varies significantly across communities. In extreme cases, entire communities could be deemed “medication deserts” because geographic access to pharmacies and the availability of the most prescribed medications within them were very poor. To our knowledge, this study is first to report on the relationship between SES and geographic access to medications using small area econometric analysis techniques. Our findings should be reasonably generalizable to other urban areas in North America and Europe and suggest that more research is required to better understand the relationship of socio-economic environments and access to medications to develop strategies to achieve equitable medication access.