Introduction: Human Immunodeficiency Virus (HIV) infection is associated with hypochlorhydria but the mechanism is unknown. The objective of this study was to determine effects of anti-retroviral therapy (ART) on gastric physiology as measured by validated markers. Methods: We studied HIV infected individuals who were either ART-naïve or on treatment with undetectable viral loads. We measured H.pylori IgG antibodies, pepsinogen (PG) 1 and 2 levels and fasting gastrin-17 using Biohit GastroPanel®. Gastric antral biopsies and juice were obtained for histology and pH respectively. Also included were historical data from HIV negative participants (n = 72) in a previous study, for reference. Results: We enrolled 84 HIV positive individuals with a median age 42 years (IQR 37-40 years). 55(66%) were female, 32(38%) were ART naïve, and 52(62%) were on ART. Hypochlorhydria (pH>4) was present in 48(57%) of the HIV positive and 18(25%) of the HIV negative individuals (OR 4: 95% CI 1.9-8.5, P<0.001) with no significant effect of ART (OR 0.9: 95% CI 0.3-2.3, P = 0.82). Hypochlorhydria was not associated with the serological detection of corpus atrophy using low PG 1:2 ratio (OR 2.1: 95% CI 0.5-10.2, P = 0.37) or GastroPanel® algorithm, (OR 0.7: 95% CI 0.01-60.1, P = 1.0). ART reduced the frequency of low PG 1:2 ratio (P = 0.001), but not the histological detection in the antrum of atrophy or non-atrophic gastritis. Conclusion: ART use is associated with reduced serological evidence of corpus atrophy but has no effect on fasting pH, supporting earlier data that suggest that the mechanism of HIV-associated hypochlorhydria is multifactorial.