Intracranial haemorrhage (ICH) is the most serious type of bleeding for patients with haemophilia. Prior published reports regarding ICH predate the widespread provision of prophylaxis. Our study objectives were to determine risk factors for ICH and whether prophylaxis reduces ICH occurrence. We performed a nested case-control study of persons with haemophilia, ≥2 years of age enrolled in the Centers for Disease Control and Prevention Universal Data Collection project. Of 10 262 patients 199 (1·9%) experienced an ICH for an incidence rate of 390/105 patient years. Head trauma was reported in 44% (88/199). ICH mortality was 19·6% (39/199). Significant risk factors for ICH included a high titre inhibitor [odds ratio (OR) = 4·01, 95% confidence interval (2·40–6·71)], prior ICH [OR = 3·62 (2·66–4·92)] and severe haemophilia [OR = 3·25 (2·01–5·25)]. Prophylaxis was associated with a significant risk reduction for ICH occurrence in patients with severe haemophilia who were negative for human immunodeficiency virus or an inhibitor, with an OR of 0·52 (0·34–0·81) and 0·50 (0·32–0·77) respectively. The most significant risk factors for ICH included the presence of an inhibitor, prior ICH, severity of haemophilia and reported head trauma. This is the first study to demonstrate that prescribed prophylaxis conferred a protective effect against ICH in patients with uncomplicated severe disease.