INTRODUCTION: Determination of the true prevalence of Helicobacter pylori (H. pylori) is difficult in a hyper-endemic area like Nigeria with use of serological tests because of their low discriminatory power between previous and current infections. The use of biopsy based methods will go a long way to mitigate this problem. We investigated the prevalence of H. pylori in dyspeptic patients and its relationship with gastroduodenal pathologies using gastric biopsy histology and rapid urease test. METHODS: Eighty-six consecutive adult patients with dyspepsia underwent upper gastrointestinal endoscopy using forward-viewing endoscopes. Antral biopsy specimens were collected for histology and rapid urease test. Diagnosis of H. pylori infection was made if both or either of the tests was positive. RESULTS: Of the 86 subjects, there were 39 (45.3%) males and 47(54.7%) females. The age range was 23 to 85 years with a mean of 49.19 plus or minus 13.75 years. Diagnosis of H. pylori was made in 55(64%) patients. Gastritis was the commonest endoscopic finding (60.5%), serious gastroduodenal pathology (gastric ulcer, duodenal ulcer and gastric cancer) were documented in only 12 (14%) patients. Thirty three (63.5%) of the 55 patients with gastritis had H. pylori infection while 7(58.3%) of the 12 patients with serious gastroduodenal lesions had the infection. Thirteen (72.2%) of the 18 patients that had normal endoscopic findings were H. pylori positive. CONCLUSION: The prevalence of H. pylori among dyspeptics using biopsy based methods is high in the South-Western part of Nigeria. It is therefore important to test and treat H. pylori among Nigerians with dyspepsia