The availability of antiretroviral medications has transformed living with HIV infection into a manageable chronic illness, and high levels of adherence are necessary. Stigma has been identified as one reason for missing medication doses. The objective of this study was to explore the relationship between perceived HIV stigma and self-reported missed doses of antiretroviral medications in a 12-month, repeated measures cohort study conducted in Lesotho, Malawi, South Africa, Swaziland, and Tanzania. Data were collected from 1457 HIV-positive individuals at three times between January 2006 and March 2007. Participants completed a series of questionnaires. Of the 1457 participants, 698 were taking ARVs during the study and are included in this analysis. There was a significant relationship between perceived HIV stigma and self-report of missed medications over time (t = 6.04, p </= 0.001). Individuals who reported missing more ARV medications also reported higher levels of perceived HIV stigma. Individuals reporting fewer medication worries reported decreased stigma over the one year period (t = -4.79, p </= 0.001). While those who reported increased symptom intensity also reported increased stigma initially (t = 8.67, p </= 0.001) that remained high over time. This study provides evidence of a significant and stable correlation that documents the relationship between perceived HIV stigma and self-reported reasons for missed medications over time. These findings suggest that part of the reason for poor adherence to ARV medications is linked to the stigma experienced by people living with HIV.