Background Current information about AIDS-related gastrointestinal cytomegalovirus end-organ disease (CMV-EOD) is scarce. The objectives of this study were to identify the prevalence and main features of gastrointestinal CMV-EOD in patients with advanced HIV disease. Methods Retrospective cohort study carried-out at a tertiary-care center in São Paulo, Brazil, from January to December 2019. We included hospitalized people living with HIV with gastrointestinal CMV-EOD, CD4 + count ≤100 cells/µL, and ≥ one quantitative detection of CMV DNA in plasma. Results Ten (3.8%) of 261 cases had gastrointestinal CMV-EOD. Nine (90%) cases were men, age median (IQR) was 44 (38–54) years, and CD4 + cell count median (IQR) was 6 (7–39) cells/µL. The 10 cases had positive quantitative detection of CMV DNA in plasma with median (IQR) of 572 (103–2 981) IU/mL. The main presenting condition was esophagitis ( n = 7, 2.7% cases). Eight (80%) cases received anti-CMV treatment, and one case died due to nosocomial pneumonia. Conclusions The prevalence of gastrointestinal CMV-EOD was 3.8%, similar to described in pre-combined antiretroviral therapy studies. Among cases with gastrointestinal CMV-EOD, all had positive quantitative detection of CMV-DNA in plasma but the values varied; esophagitis was the most common presentation, and all but one were discharged from the hospital.