This study was designed to evaluate a novel modification of the non-invasive capsule-based 13C-urea breath test (13C-UBT). 114 patients were tested for Helicobacter pylori (HP) infection with the use of only 38 mg 13C-urea administrated in solid capsulated form. Obtained results were compared with tissue based methods: histology and rapid urease test (CLOtest). Results of histology and/or CLOtest were considered as the gold standard for each patient. In addition, also capsule-based, micro-dose (37kBq) 14C-urea breath test (14C-UBT) was performed. With a cut-off for delta-over-base values of 5/1000 (i.e., 5 per mil), 13C-UBT results (measured by non-dispersive infrared spectroscopy, NDIRS) correlated highly significant with combined results for invasive methods i.e., CLOtest + histology score. Compared with histology, CLOtest, and the gold standard, the diagnostic values of the test were: sensitivity 97%, specificity 95%, with positive and negative predictive values about 90% and 98% respectively. The modified 13C-UBT test was found to be in full concordance with 14C-UBT; there was 100% agreement in the diagnostic classification of all positive (89) and negative (25) patients. Described modification of 13C-UBT showed that presented modification of 13C-UBT is an excellent, simple, low cost, non invasive, and safe diagnostic tool in HP detection and should be recommended particularly in cases when the use of radioactive urea is contraindicated.