Summary Objectives This study determined the prevalence of Campylobacter spp., Helicobacter pylori and Arcobacter spp. in stool samples from Venda in relation to diarrhea, intestinal inflammation and HIV status using specific molecular methods. Methods Stool samples were collected from hospital patients (255) and primary school children (67). Genomic DNA was extracted from the stools and molecular methods including PCR, PCR followed by restriction analysis and multiplex PCR were used to test for the different organisms. The lactoferrin content of the stools was determined using commercial kits from TechLab (Blacksburg, VA, USA). Results The prevalence of the different organisms was 50.6% for H. pylori , 10.2% for C. jejuni , 6.2% for A. butzleri , 6.5% for C. coli , 3.1% for C. concisus , 2.8% for A. cryaerophilus and 1.9% for A. skirrowii . Of all the organisms, only C. jejuni was significantly associated with diarrhea (84.8%) ( χ2 = 21.025, P < 0.001) and elevated levels of lactoferrin (78.8%) ( χ2 = 16.919, P < 0.005) and was an important pathogen associated with diarrhea among HIV positive individuals (22.8%). Conclusions Campylobacter infections are common causes of gastroenteritis in Venda. Non- C. jejuni / coli Campylobacters such as C. concisus as well as A. butzleri and H. pylori may be involved in gastrointestinal diseases in the region but further studies are needed to confirm this hypothesis.