In HIV-infected patients, manifestations of the disease are common in the gastrointestinal tract. The objective of our study was to evaluate the diagnostic yield of the Given®Video Capsule System (Given Imaging, Yoqneam, Israel) in these patients. After exclusion of GI-tract stenosis by anamnestic exploration, 49 patients were included into the study. Stratification: Group A (n = 19): HIV-positive, CD4cell count < 200/μl, gastrointestinal symptoms present. Group B: HIV-positive, CD4< 200/μl, without gastrointestinal symptoms (n = 19 Group) C: healthy volunteers (n = 11). In group A there was a total of 30 pathological findings, 15 of which with therapeutic implications. In group B, there was a total of 22 pathological findings, 5 relevant for therapy. In group C there was a total of 13 pathological findings, 3 with therapeutic relevance. In 89% (group A) vs. 26% (group B), pathological findings were detected distal the ligament of Treitz (p = 0.001). All capsules were recovered without complications after 12 to 96 h from the stool. Wireless capsule endoscopy of the small intestine should be considered for HIV-infected patients with marked immunosuppression and gastrointestinal symptoms.