Objective To determine if changes in chromosome 7 and 17 copy number can be used to predict recurrence in patients with primary noninvasive (pTa) or superficially invasive (pT1) transitional cell carcinoma (TCC) of the urinary bladder. Patients and methods Tissue specimens for 129 tumours from 52 patients (38 men and 14 women) with pTa/pT1 TCC at first diagnosis were retrieved from pathology archives. All patient notes were accessed and disease outcome documented for superficial (pTa/pT1) recurrence or progression to detrusor muscle invasion ( pT2). The tumours were examined for chromosomal copy number of chromosomes 7 and 17 using fluorescence in situ hybridization (FISH) with chromosome‐specific probes. The copy number of chromosomes 7 and 17 was determined in interphase nuclei on intact 6 µm tissue sections. Results Aneusomy of chromosomes 7 and 17 was detected in the index primary tumours of 10 of 32 (31%) patients with subsequent recurrent disease. No aneusomy for these chromosomes was detected in primary tumours from 20 patients with no detect‐able recurrence ( P = 0.0082). The relative risk of recurrence was 3.62 times greater (95% confi‐dence interval 1.6–8.1, Cox’s multiple regression P = 0.0019) for patients with chromosomal aneusomy in primary TCC. Neither stage nor grade of the primary tumours was associated with recurrence in these patients, nor was there a significant association with increased grade (G2/3) or stage ( pT2) at recurrence. Conclusion These results suggest that the measurement of aneusomy by FISH, using markers for chromosomes 7 and 17, predict recurrence in a subgroup of patients with pTa/pT1 tumours at presentation. This finding may offer a new objective and quantitative test for patients destined to recur.