Fluorescence in situ hybridization (FISH) is regarded as a potential new tool for the clinical management of bladder cancer that works by detecting cytogenetic aberrations in noncycling, exfoliated cells from bladder irrigations. However, clinical validation steps must be addressed to define the true predictive potential in a clinical setting. Toward the validation of FISH with the use of bladder washings and prior to incorporation into a large, prospective clinical trial, a pilot study was designed to determine its clinical potential, define testing limitations, optimize a panel of probes specific for bladder cancer detection, and outline protocol/data collection parameters. Correlations with standard cytogenetics and clinicopathological features of bladder cancer were investigated. Exfoliated cells obtained from benign bladder washings served as normal controls. The results of this pilot study suggest the following: (a) FISH and cytology are complementary testing procedures; however, the FISH data provided valuable ploidy and specific genotypic information for recurrent tumors in "suspicious" cases; (b) chromosomal aberrations defined by FISH are associated with tumor grade and stage (i.e., simple numerical aberrations were associated with low-grade tumors, and high-grade and invasive tumors exhibited multiple, nonrandom chromosomal aberrations and vast intratumor heterogeneity); (c) somatic pairing or homologous centromeric association can give a false-positive result and appears to be linked to prior therapy; (d) dual hybridization with reference gene-specific probes must be used to control for somatic pairing; and (e) focal, deep muscle invasive lesions, with no surface exposure, may yield false-negative results. The data suggest that FISH analysis, with the use of cells isolated from bladder washings, is a powerful technique holding promise for early cancer detection, monitoring treatment outcome, and predicting recurrence of disease.