To study the involvement of DNA mismatch repair genes in non‐small cell lung cancer, matched normal and tumoral DNA samples from 31 patients were analyzed for both LOH and microsatellite instability with 34 markers at or linked to hMLH1(3p21),hMSH2(2p16), hMSH3(5q11‐q13),hMSH6(2p16), hPMS1(2q32), and hPMS2 (7p22) loci. Chromosomal regions 3p21 and 5q11‐q13 were found to be hemizygously deleted in 55% and 42% of the patients, respectively. Sixty five percent of the patients deleted at hMLH1 were also deleted at hMSH3. The shortest regions of overlap for 3p21 and 5q11‐q13 deletions delimited by D3S1561/D3S1612 and D5S2107/D5S624, respectively, were restricted to genetic distances of only 1 cM. Currently, the hMLH1 (3p21) and hMSH3 (5q11‐q13) genes are the only known candidates located within these regions. The mutational analysis of hMLH1 and hMSH3 in hemizygously deleted patients led to the detection of 2 new polymorphisms in hMSH3. The consequence of these allelic losses remains unclear, but the lack of inactivating mutation might explain that replication error, the hallmark of mismatch repair genes inactivation in cancer cells, was quasi‐absent in tumors. We suggest that hMLH1 and hMSH3 genes could be involved in lung tumorigenesis through dosage effect in cellular functions other than replication error correction. Int. J. Cancer 77:173–180, 1998. © 1998 Wiley‐Liss, Inc.