Objective: To describe incidence and clinical characteristics of bacille Calmette–Guérin (BCG) infections after BCG bladder instillation amongst patients with non-muscle-invasive bladder cancer in Denmark. Patients and methods: We conducted a nationwide register-based cohort study in Denmark between 2002 through 2017. Patients with BCG infection were identified by cross-linking data from the Danish National Hospital Registry on patients treated with BCG instillations and patients diagnosed with tuberculosis according to the International Classification of Diseases 10, and data obtained from International Reference Laboratory of Mycobacteriology. Hospital records were reviewed for clinical information. Results: During the study period, 6753 patients (5281 men; mean [SD] age 71.1 (0.1) years) received BCG instillations, of which 66 patients (1%) developed BCG infections. There were no differences in age or Charlson Comorbidity Index between the patients in the study population stratified by BCG infection. The median (interquartile range) time from first BCG instillation until symptoms of BCG infection was 169.5 (38–585) days. Extrapulmonary localisation of BCG infections (37 patients, 56.1%) was significantly more frequent than pulmonary BCG infections (20 patients, 30.3%; P < 0.001). The most common extrapulmonary localisation was the genitourinary tract (29 patients, 78.4%). Conclusion: BCG infections after bladder instillation are rare, mainly affect male patients, and are most frequently extrapulmonary. BCG infections should be suspected despite a long time span between occurrence of symptoms and prior bladder instillation.