Urinary tract infections have been linked with urinary tract cancer, but the association remains controversial. We examined whether pyelonephritis is a clinical marker of urogenital cancer. We used Danish medical databases to create a population-based cohort of patients with an incident hospital-based pyelonephritis diagnosis during 1994–2013. Follow-up for cancer began at pyelonephritis diagnosis and ended on 30 November 2013. We restricted the cohort to patients older than 50 years, as urogenital cancer risk in the younger population is low. We calculated the absolute risk of urogenital cancer and the standardized incidence ratio (SIR) comparing risk observed in pyelonephritis patients to risk expected in the general population of Denmark. Among 15 070 patients with pyelonephritis, we observed 197 urinary tract cancers and 374 genital organ cancers over a 20-year follow-up period. The absolute risk of urogenital cancer was 1.5% 6 months after a pyelonephritis diagnosis, and the cumulative risk was 3.0% at 5 years. During the first 6 months following a pyelonephritis diagnosis, the SIR of urogenital cancer was 8.56 (95% CI 7.49–9.75). Between 6 and 12 months following this diagnosis, the SIR was 1.75 (95% CI 1.26–2.35), and beyond 1 year the SIR was approximately unity for most cancers. Notably, the SIR for bladder cancer among women remained elevated beyond 1 year of follow-up. Patients presenting with a hospital-based diagnosis of pyelonephritis had a higher 6-month risk of urogenital cancer than expected. However, causation cannot be inferred because of the study design.