The diagnosis of Helicobacter pylori (H. pylori) infection by GC-MS detection of the (CO2)-C-13 enrichment in C-13-urea breath test (C-13-UBT) samples is reported. This study aimed to optimize the C-13-UBT with regards to the diagnostic cut-off value, sampling time, and frequency. The H. pylori status of 103 dyspeptic patients was obtained by histological examination, the rapid urease test as well as with the GC-MS C-13-UBT. Analytical and diagnostic accuracies were determined by comparison of the GC-MS C-13-UBT results with that of the analytical and diagnostic gold standards, namely GC-isotope ratio MS (IRMS) and histology. The (CO2)-C-13 enrichment values obtained with GC-MS analysis, correlated favorably (r(2) = 0.993) with those obtained by GC-IRMS analysis. When compared to histology, the GC-MS C-13-UBT had a diagnostic sensitivity of 92% and a specificity of 93%. The positive predictive value (PPV), negative predictive value (NPV), and accuracy were 95, 89, and 92%, respectively. It was concluded that SIM GC-MS is capable of analyzing nonradioactive C-13-UBT samples, with a precision and accuracy sufficient to distinguish between H. pylori positive and negative patients.