Gastric biopsies from 65 Costa Rican dyspeptic patients were investigated for the presence of Helicobacter pylori DNA by polymerase chain reaction (PCR) amplification of 16S rRNA sequences. Both frozen and paraffin-embedded samples were used, and the results were compared with bacterial culture and histological examination. Helicobacter pylori DNA was detected by PCR in 60 (92%) of the patients, and Helicobacter pylori strains confirmed by PCR could be isolated from 37 of them. Altogether, 59 patients were shown to be infected using the combination of culture and histology as the reference method. The sensitivity of PCR analysis of frozen material was 98% (58/59). The PCR analysis of paraffin-embedded samples seemed less reliable than that of frozen biopsy material.