Objective To identify Helicobacter pylori and major virulance factor, cagA, in patients with laryngeal diseases and nasal polyps. Study Design Cross-sectional study with planned data collection. Setting The study was performed on fresh tissue samples from patients with 32 nasal polyps, 29 normal nasal mucosa, and 27 laryngeal diseases presenting to the Otolaryngology–Head and Neck Surgery department of a major military hospital in Istanbul, Turkey. Subjects and Methods Tissue specimens were evaluated by in-house polymerase chain reaction (PCR) and real-time PCR for bacterial DNA and by real-time PCR for cagA. The impact of commercial and in-house DNA extraction methods was also evaluated. Results H pylori DNA was detected only by real-time PCR in 59.4 percent of nasal polyps, 70.4 percent of nasal mucosa samples, and 58.6 percent of larynx samples. cagA was identified in 78.9, 89.5, and 82.4 percent of positive polyp, nasal mucosa, and larynx samples, respectively. No statistically significant differences were observed between groups. DNA purification methods were equally effective. Conclusion H pylori DNA is present in nasal polyp and larynx tissues as well as normal nasal mucosa, as detected by a sensitive real-time PCR assay. cagA-positive strains dominate in all groups.