Previous studies have implicated human adenovirus 36 (Adv36) as a potential contributor to overweight and obesity. People living with HIV have an altered body composition compared to healthy individuals. There is still no evidence to confirm the relationship of Adv36 as one of the causes of lipohypertrophy. The main objective of this study was to verify the viral Adv36 infection as a factor associated with the presence of lipohypertrophy in HIV-infected individuals. A case-control study on people with HIV treated at a specialized public health service in southern Brazil. Subjects underwent interviews, diagnostic tests, and anthropometry to determine lipodystrophy and its classification. Demographic and clinical data were examined to investigate the presence of Adv36. The cases were participants with lipohypertrophy, and the controls were eutrophic participants. 101 participants were included (38 cases and 63 controls), and the frequency of Adv36 infection was 10.9%. There was a statistically significant association between lipohypertrophy and the female sex (p < 0.001), and a trend for the presence of Adv36 (p = 0.059) and lipohypertrophy. After adjustment for confounders, Adv36 has not considered an independent risk factor for lipohypertrophy. Lower levels of glucose were associated with Adv36 infection. There was a significant association between lipohypertrophy and the female sex, and no association with lipohypertrophy and Adv36, perhaps due to the small sample size.