Helicobacter pylori (H. pylori) has been found to be associated with various gastrointestinal diseases. Confirmation of H. pylori infection includes invasive and non-invasive methods. There has been increasing interest in noninvasive tests recently. However, the geographical differences among H. pylori strains have been emphasized recently and the H. pylori strain in Taiwan showed a high cagA positive result and different vacA subtype when compared with those of Western countries. The aim of this study is to access and compare the reliability and the diagnostic accuracy of the stool H. pylori antigen tests by spectrophotometry and by the visual method, especially in Southern Taiwan. Thirty-two patients (18 men and 14 women; age range: 23-91 y/o, mean: 50.5 y/o) who underwent gastroendoscopy at Kaohsiung Medical University Hospital were enrolled in this study. H. pylori infection status was confirmed by culture or two positive test results on CLO test, histology and 13C-urea breath test (13C-UBT). The exclusion criteria included previous gastrointestinal tract surgery, use of antibiotics, proton pump inhibitor or compounds containing bismuth within 1 month of the study. Among them, 14 patients were with duodenal ulcer (DU), 4 with gastric ulcer (GU), 12 with non-ulcer dyspepsia, and 2 with GU and DU. Those patients had their stool collected for ELISA tests of H. pylori stool antigen (HpSA). The HpSA tests were positive in 16 of 18 patients diagnosed as H. pylori positive, and negative in 13 of 14 patients as H. pylori negative. The sensitivity and specificity were 88.9% and 92.9% respectively. The positive and negative predictive values were 94.1% and 86.7% respectively. The concordance of HpSA accessed by spectrophotometry and visual method is 100%, which makes this test even easier and cheaper. We concluded that stool HpSA test is a noninvasive, accurate, reliable, rapid and easy way to diagnose H. pylori infection in Southern Taiwan, either by spectrophotometry or by visual assessment.