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Purpose: The study aims to find candidate probes of fluorescence in situ hybridization (FISH) for detection of lung cancer with bronchial brushings and to evaluate whether the accuracy of diagnosing lung cancer by cytological deviant and genetic abnormalities is greater than that of cytology alone. Methods: Centromeric enumeration probes (CEPs) for chromosomes 2, 3, 6, 7, 8, 9, 11, 12, and 17 were analyzed using FISH in 74 surgical resection tissues, 32 operative margin tissues without tumor involvement of lung cancer, and 174 bronchial brushings. Results: The aneuploidy rates of the tested probes were 61.7, 89.1, 80.0, 92.7, 65.0, 70.4, 66.7, 71.8, 68.9 % in tumor tissues, and 29.3, 58.9, 33.3, 69.6, 67.0, 40.3, 38.0, 49.3, 35.1 % in bronchial brushings. The combination of cytology and FISH using the three-probe set for chromosomes 3+7+8 significantly improved the sensitivity of bronchial brushing examination for lung cancer detection ( P = 0.00003), especially squamous cell carcinoma (SCC), which increased from 78.0 to 98.2 %. The specificity of the 3+7+8 probe set was 94.6 %. Moreover, a high aneuploidy rate of the probe set in bronchial brushings was detected more often in SCCs ( P = 0.029) and late-stage non-small-cell lung cancer (NSCLC) ( P = 0.044). Kaplan-Meier curves indicated that adenocarcinoma (ADC) patients with high aneuploidy rate of CEP3 in tissue samples exhibited poorer overall survival ( P = 0.016). Conclusions: FISH performed on cytology preparations is useful for confirmation of cancer diagnosis. The three-probe set, 3+7+8, has potential value for the detection of SCCs in bronchial brushings. [ABSTRACT FROM AUTHOR]