Background. Many countries with high prevalence of human immunodeficiency virus (HIV) infection also have substantial Muslim populations. HIV-infected patients who travel to Hajj in Saudi-Arabia may encounter challenges regarding their anti-retroviral therapy (ART). Methods. In a cohort study in Nigeria, clinically stable patients on ART who were traveling for the 2008 to 2009 Hajj (Hajj-pilgrims [HP]) were selected and compared with consecutively selected Muslim patients who were clinically stable and traveled to and from distances within the country to access ART (non-pilgrims [NP]). Participants were clinically evaluated and interviewed regarding their adherence to ART pre-travel and post-travel, international border passage with medications and reasons for missing ART doses. Post-travel change in CD4 counts and RNA-PCR viral load were measured. Outcomes were proportion who missed >= 1 dose of ART during Hajj compared with pre-travel or post-travel and failure of ART, defined as decline in CD4 cell counts or high viral load or both. Results. Thirty-one HP and 27NP had similar characteristics and were away for (median [range]) 36 days (28-43 days) and 84 days (28-84 days), respectively (p < 0.0001). Those who missed >= 1 ART doses among HP and NP while away were 16/31 (51.6%) and 5/27 (18.5%), respectively with risk ratio (95% confidence interval [CI]) 2.79 (1.18-6.60). Among HP, the proportions who missed >= 1 ART doses pre-travel and post-travel were lower than those who missed it during Hajj. Those who failed ART among HP compared with NP were 15/31 (48.4%) and 5/27 (18.5%), respectively with odds ratio (95% CI) 4.13 (1.10-17.21). Reasons for missing ART included forgetfulness, exhaustion of supplies, stigma, spiritual alternatives, or disinclination; five patients were unable to cross airports with medications. Conclusions. Patients who went on Hajj were more likely to miss medications and to have ART failure due to several reasons including inability to cross borders with medications.