The aims of this study were to determine the levels of procalcitonin (PCT) and C-reactive protein (CRP) in Helicobacter pylori-positive (HP+) patients diagnosed with duodenal and gastric ulcer and to evaluate the correlation of PCT and CRP levels with other invasive and non-invasive diagnostic methods for determination of H. pylori eradication in post-treatment follow-up. Thirty-five HP+ patients with dyspepsia were included in this study. Serum samples (5 ml) were collected at admission and after 24 h. Antimicrobial therapy (omeprazole, amoxycillin and clarithromycin) was given for 1 week to HP+ patients who were positive only by culture or by urease test plus pathology. After 1 month, serum samples (5 ml) were collected again and culture, urease and pathology investigations were performed on endoscopic samples. PCT and CRP levels were measured in the collected blood samples. Thirty-five H. pylori-negative (HP-) cases with dyspepsia, 38 cases with bacteraemia. and 35 healthy blood donors were included in this study as control groups. The mean and minimum-maximum levels of PCT were 1(.)39 (0(.)25-6(.)75), 0(.)35 (0(.)12-0(.)71), 7(.)45 (0(.)68-51(.)5) and 0(.)40 (0(.)12-0(.)71) ng ml(-1) for the groups of HP+, HP- and bacteraemia patients and healthy donors, respectively. Mean CRP levels were 1(.)00 (<0(.)5-8(.)11), 0(.)62 (<0(.)5-3(.)2), 11(.)5 (3(.)2-43(.)5) and 0(.)63(<0(.)5-5(.)46) mg dl(-1) for the same groups. A statistically significant difference was found between HP+ patients and both HP- cases and healthy blood donors for PCT levels, and higher PCT levels were found on admission in cases of bacteraemia than in the other groups (P<0(.)05). PCT levels of HP+ cases decreased significantly (from 1(.)39 to 0(.)86) between admission and the post-treatment period (30 days); however, PCT levels remained higher than the cut-off value (0(.)5 ng ml(-1)). Similar ranges of CRP levels were found over the same time-period. The sensitivity of PCT was found to be higher than that of CRP on admission, but the specificity of PCT was found to be lower than that of CRP on the day of admission (65 and 74 %, respectively). The sensitivity of PCT was the same as that of CRP for the post-treatment period, but specificity of PCT was higher than that of CRP for the post-treatment period (83 and 76 %, respectively). It was concluded that PCT and CRP are not very effective markers for H. pylori infection in primary diagnosis or in eradication follow-up after therapy when used in parallel with conventional diagnostic methods, even if there is a difference in PCT and CRP levels between HP+ and HP- cases on admission.