Urinary polyomavirus subtype BK (BKV)-infected urothelial and renal tubular cells, "decoy cells," have been shown to be aneuploid with digital image analysis (DIA). We wanted to determine whether decoy cells cause false-positive fluorescence in situ hybridization (FISH) results in BKV-infected urine samples. Urine samples from 38 renal transplant recipients were split 3 ways and evaluated for number of decoy cells per 10 high-power fields by routine cytology, total nuclear DNA content by DIA, and chromosomal abnormalities by FISH. For DIA, Feulgen-stained cells were quantified with a CAS 200 image analyzer (Bacus Laboratories, Lombard, IL), and for FISH, the UroVysion probe set (Vysis, Downers Grove, IL) consisting of chromosome enumeration probes 3, 7, 17, and locus-specific identifier probe 9p21 (p16 gene) was used. Of the 38 specimens, 32 (84.2%) had evidence of BKV infection by routine cytology. DIA and FISH results were aneuploid/aneusomic in 30 (93.8%) and 4 (12.5%) cases, respectively. All aneusomic FISH specimens occurred in men older than 52 years of age and who also had 4 of the 6 highest PCR-BKV titers. To date, no patient has clinical evidence of malignancy. The 6 specimens without decoy cells were DNA diploid/disomic by DIA and FISH. Abnormal FISH results of urinary decoy cells occur much less frequently than aneuploidy by DIA in renal transplant recipients and might merit close follow-up in some transplant recipients.