The Helicobacter pylori (H. pylori) load in both stomach and stool and the resulting severity of gastritis are important criteria in validating the status of H. pylori infection. We aimed to assess the reliability of the H. pylori stool antigen (HpSA) test for the primary diagnosis of H. pylori infection by calculating the best cut-off value to obtain the highest sensitivity and specificity in dyspeptic patients. We also investigated the correlation of HpSA test with the severity of gastritis and H. pylori load. The H. pylori statuses of 95 patients were evaluated by the positivity of both rapid urease test and microscopic detection of H. pylori in biopsy specimens, 88 subjects of whom were H. pylori positive. The sensitivity and specificity of the HpSA test were 51.1% (45/88) and 100% (7/7), respectively, according to the manufacturer's recommended cut-off value of 0.16. However, with the best cut-off value of 0.048, calculated by receiver operator characteristics analysis, the sensitivity of the test increased to 92.0% (81/88) with the same specificity. High values of the HpSA test were correlated with high scores of corpus H. pylori load and the severity of antrum and corpus inflammation (p < 0.05). With the best cut-off value of the HpSA test, the primary diagnosis of H. pylori infection can be made with higher sensitivity and specificity. The HpSA test is a helpful tool that evaluates the severity of H. pylori infection and the degree of gastric inflammatory activity and gastric H. pylori load.