The chromosomal imbalances in nine cases of primary non-small cell lung cancer (NSCLC) and two cell lines derived from normal human bronchial epithelial (HBE) tissue were identified by comparative genomic hybridization (CGH). Gain of material from 3q and loss of 3p material were the most frequent changes in the primary tumors. Other commonly found imbalances included gain of material from 1q, 7p, 8q, 9q, 17q and 20q, and losses involving 4, 5q, 8p, 10 and 13q. High level gain was found in two cases, both encompassing the 3q23-q27 region. Loss of 3p was also found in both of the HBE cell lines suggesting that loss of one or more tumor supressor genes on 3p may be important for epithelial transformation and could be involved in the earlier stages of lung cancer development.