Health-related vulnerabilities associated with deportation are understudied. We conducted a cross-sectional study to identify factors associated with history of deportation from the US to Mexico among HIV-positive Latinos. From 2009 to 2010, we recruited a convenience sample from HIV clinics in San Diego, US and Tijuana, Mexico. Of 283 participants, 25% reported a prior deportation. Factors independently associated with increased odds of deportation history were being male [adjusted odds ratio (AOR) 2.77; 95% CI 1.18-6.48], having ≤high-school education (AOR 3.87; 95% CI 1.84-8.14), ever using cocaine (AOR 2.46; 95% CI 1.33-4.57), and reporting personalized HIV-stigma: "some have told me HIV is what I deserve for how I lived" (AOR 2.23; 95% CI 1.14-4.37). Lower self-reported antiretroviral medication adherence (AOR 0.35; 95% CI 0.12-0.96) and perceiving HIV-stigma: "most people believe a person who has HIV is dirty" (AOR 0.49; 95% CI 0.25-0.94) were associated with decreased odds of deportation history. Deportation is associated with specific socioeconomic indicators that are known to impact the health of individuals living with HIV.