Objective: Ileal conduit urinary diversion (ICUD) is the most common procedure after radical cystectomy. Although complications have been reported, few patients with ICUD and bladder preservation controls have been available for long-term follow-up. This study compared the long-term effect of structural changes after cystectomy with ICUD to that in bladder preservation controls. Design:: A retrospective nationwide cohort study. Setting:: Data retrieved from the Taiwan National Health Insurance Research Database. Participants:: The National Health Insurance database was explored for patients diagnosed with bladder cancer between 1997 and 2006. Only cancer-free patients without chemotherapy and other types of urinary diversion who lived for >5 years were included in the analysis. Outcome measures: Patient characteristics, comorbidity and postoperative urinary tract disease were statistically analysed and compared. Cox proportional hazards model was used to evaluate the incidence rates of outcomes after adjustment for covariates. Propensity scores analysis was used to balance the clinical parameters between groups. The primary outcomes were postoperative new-onset urinary tract disease such as urinary tract infection (UTI), UTI with septicaemia and chronic kidney disease (CKD), or calculus of kidney and ureter. Results: There were 11 185 patients included in our cohort, among which 703 (6.3%) and 10 482 (93.7%) patients received ICUD and bladder preservation procedure, respectively. Compared with patients who only underwent a bladder preservation procedure, those who had undergone ICUD after cystectomy were independently associated with postoperative de novo urinary tract disease. Propensity score analysis (1:4) was also performed. ICUD contributed to significantly higher new-onset UTI, UTI with sepsis and CKD (HR=1.30, 3.16, 1.35, respectively) compared with bladder preservation procedure after adjustment for age, gender and comorbidities. Conclusion: ICUD after radical cystectomy was associated with a higher incidence of UTI, UTI with septicaemia and CKD during long-term follow-up than the incidences following a bladder preservation procedure.