Roentgenographically occult bronchogenic squamous cell carcinomas are early lung cancers that localize mainly within the bronchial wall and are thought to be a good model for elucidating chromosomal alterations during lung cancer progression. In this study, we analyzed allelic losses on chromosome regions 1p36, 3p14.2, 9p21, 10q25.3-q26.1, 13q14.12-q14.2, and 16q24.1-q24.2, in which there are putative tumor suppressor genes that may play roles in lung carcinogenesis. Forty-five cases with roentgenographically occult bronchogenic squamous cell carcinoma (ROC) and 47 cases of bronchogenic carcinoma with abnormal shadows (roentgenographically nonoccult bronchogenic squamous cell carcinoma [RNOC]) were examined. Highly frequent LOHs in both ROCs and RNOCs were observed in chromosome regions 3p14.2, 9p21, and 13q14.1-q14.2. LOHs were more frequently observed in RNOCs than in ROCs at two loci: 10q25.3-q26.1 and 16q24.1-q24.2. These results suggested that (1) putative tumor suppressor genes exist on 3p14.2, 9p21, 10q25.3-q26.1, 13q14.12-q14.2, and 16q24.1-q24.2, which may play important roles in lung carcinogenesis; (2) mutations in genes at 3p14.2, 9p21, and 13q14.12-q14.2 represent rather early events in lung carcinogenesis; and (3) mutations in genes on 10q25.3-q26.1 and 16q24.1-q24.2 represent rather late events.