Inactivation of the FANC–BRCA pathway via promoter methylation of the FANCF gene renders cells sensitive to DNA crosslinking agents, and has been identified in ovarian cancer cell lines and sporadic primary tumor tissues. We investigated epigenetic alterations in the FANC–BRCA pathway in head and neck squamous cell carcinomas (HNSCC) and non-small-cell lung cancers (NSCLC) using methylation-specific PCR. Promoter methylation of FANCF occurred in 15%(13/89) of HNSCCs and 14%(22/158) of NSCLCs. Methylation of BRCA1 occurred only in 6/158 NSCLC, and was limited to adenocarcinomas and large-cell carcinomas of the lung. No methylation of BRCA2 was detected. FANCF methylation was associated with a shorter duration of tobacco use (P= 0.03) and a younger age of starting smoking (P= 0.06) in NSCLC, and with a greater number of years of alcohol drinking (P= 0.02) in HNSCC. In adenocarcinomas of the lung, FANCF promoter methylation was a significant predictor of poor survival with a hazard ratio of 3.1 (95% CI 1.2–7.9). This study demonstrates that inactivation of the FANC–BRCA pathway is relatively common in solid tumors and may be related to tobacco and alcohol exposure and survival of these patients.