Roentgenographically occult bronchogenic squamous cell carcinomas are early lung cancers that localize in the bronchial wall, and are thought to be a good model to elucidate the carcinogenesis of lung cancer. In the present study, we analyzed the incidence of allelic losses on chromosome regions 3p21 and 17p13 in 40 cases of roentgenographically occult bronchogenic squamous cell carcinomas, using three microsatellite dinucleotide polymorphic markers. We also investigated the relationship between such allelic loss and the clinicopathological findings of those cases. These chromosome regions showed frequent losses. Moreover, the incidence of loss on 17p13 increased gradually along with the advance of the depth of invasion, while the incidence of loss on 3p21 increased along with the advancing length of the longitudinal extension. These results suggested that these chromosome regions play different roles in lung cancer progression, i.e., the 3p21 chromosome region was related to the longitudinal extension of the carcinoma while the 17p13 (p53) region was related to the depth of invasion.