Objectives To compare catastrophic injury rates between the 14 South African Provincial Rugby Unions. Design A prospective, population-based study conducted among all South African Unions between 2008–2014. Methods Player numbers in each Union were obtained from South African Rugby's 2013 Census. Catastrophic injuries were analysed from BokSmart's serious injury database. Incidence rates with 95% Confidence Intervals were calculated. Catastrophic injuries (Acute Spinal Cord Injuries and catastrophic Traumatic Brain Injuries) within Unions were compared statistically, using a Poisson regression with Incidence Rate Ratios (IRR) and a 95% confidence level (p < 0.05). Results Catastrophic injury incidence rates per Union ranged from 1.8 per 100 000 players (95% CI: 0.0–6.5) to 7.9 (95% CI: 0.0–28.5) per 100 000 players per year. The highest incidence rate of permanent outcome Acute Spinal Cord Injuries was reported at 7.1 per 100 000 players (95% CI: 0.0–17.6). Compared to this Union, five (n = 5/14, 36%) of the Unions had significantly lower incidence rates of Acute Spinal Cord Injuries. Proportionately, three Unions had more Acute Spinal Cord Injuries and three other Unions had more catastrophic Traumatic Brain Injuries. Conclusions There were significant differences in the catastrophic injury incidence rates amongst the Provincial Unions in South Africa. Future studies should investigate the underlying reasons contributing to these provincial differences.