Background: Transurethral resection of bladder tumor (TURBT) combined with intravesical Bacillus Calmette-Guerin (BCG) perfusion is a widely accepted treatment for moderate or high risk non-muscularinvasive bladder cancer (BCa). Despite its effectiveness, the recurrence and progression rate of tumor are still high. We evaluated the predictive role of fluorescence in situ hybridization (FISH) for the response to BCG perfusion in BCa.Methods: Patients with BCa who underwent BCG perfusion and FISH test in our hospital were selected. Logistic regression and Kaplan-Meier methods were used to evaluate the relationship between FISH results and tumor recurrence or progression. COX proportional hazards regression analysis was used to identify risk factors for recurrence or progression. SPSS (version 24.0, IBM Corporation) was used for statistical analysis.Results: Seventy-six patients were included in this study, with a median age of 63.0 (55.0-70.0) years, and a median follow-up time of 19.0 (7.5-29.0) months. Fifteen patients relapsed after BCG perfusion. Before TURBT, 39 patients were positive for FISH and 20 were negative. There was no significant difference in the recurrence rate of BCG after perfusion predicted by preoperative FISH positive (10.3% vs. 10%, P=0.675). No association was found between preoperative FISH and tumor recurrence (P=0.955) or disease progression (P=0.186). After BCG perfusion, 10 patients were FISH positive and 14 patients were FISH negative. There was significant difference in recurrence rate of BCa predicted by positive FISH (100% vs. 7.1%, P<0.001). FISH results were significantly associated with tumor recurrence (P<0.001) and disease progression (P=0.001). Kaplan-Meier and univariate COX proportional hazards regression analysis clarified that FISH positive after BCG perfusion, tumor-node-metastasis (TNM) stage, and multiple tumors were risk factors for tumor recurrence and progression (P<0.05). Tumor TNM stage and FISH positive after BCG perfusion were independent risk factors for recurrence.Conclusions: Positive FISH after BCG perfusion can well predict the risk of recurrence and progression of BCa, and recurrence within six months is more likely. After BCG perfusion, it is better to recommend close follow up in patients with positive FISH.