The 13C-urea breath test (13C-UBT) for diagnosis of Helicobacter pylori (Hp) infection was evaluated in 41 patients after partial gastrectomy and was used for determination of the Hp-prevalence after two different procedures of reconstruction of the gastrointestinal tract, i.e. Billroth's II operation and Roux-en-Y anastomosis. Breath samples were taken at various time points within 30 minutes after a motility inhibiting liquid test meal with citric acid followed by 75 mg of 13C-urea. The 13CO2/12CO2-ratio (delta-value) was measured using isotope ratio mass spectrometry and the recovery of tracer in the exhaled breath was calculated (UBT-value). In all patients and in the corresponding control groups comparison of established reference methods (culture, CLO test, and Fuchsin staining) with the 4 point breath analysis for detection of Hp was investigated. In patients with partial gastrectomy, the sensitivity of the 13C-UBT to detect the presence of Hp and the negative predictive values were 100%, whereas the specificity and the positive predictive values were about 80%. In patients without gastric surgery quality control parameters were not significantly different. Hp-prevalence in postoperative patients was about 45%. All results were independent of their expression either as delta-value or as UBT-value and were not significantly different between the patients with Billroth's II operation and the patients with Roux-en-Y anastomosis. In conclusion, the 13C-UBT is a suitable method for diagnosis and therapeutic monitoring of Hp-status in patients after partial gastrectomy.