Background This study compared long-term outcomes of biological and mechanical mitral valve replacement (MVR) in patients requiring replacement of the mitral valve where repair was not feasible. Methods A single-centre registry of patients receiving MVR between 2005 and 2015 was established. Thirty-day mortality and long-term outcomes were analysed and compared. Results Three hundred twenty four patients underwent MVR (265 biological; 59 mechanical valves). Patients receiving biological valves were older ( p < 0.001), had a higher log EuroSCORE ( p < 0.001) and received less minimally invasive surgery ( p < 0.001). Immediate procedural mortality was 1.9%, which only occurred in the biological valve group. At 30 days, 9.0% of patients had died, 4.0% experienced stroke, 8.0% received a pacemaker and 10.5% suffered an acute renal failure. The rate of re-thoracotomy (14.2%) was lower in the biological (12.5%) than in the mechanical valve group (22.0%; adjOR 0.45 [0.20–1.00]; p = 0.050). Frequent long-term complications were stroke (9.2%) and bleeding (4.8%), with bleeding complications being higher in the mechanical valve group ( p = 0.009). During the follow-up period biological valves showed a numerically higher survival rate during the first years, which shifted after 3 years in favour of mechanical valves. At 10 years, survival rates were 62.4% vs. 77.1% in the biological and mechanical valve groups ( p = 0.769). Hazard ratio after adjustment was 0.833 (95% CI 0.430–1.615). Conclusion These data confirm that mechanical valve implantation is associated with an increased risk of bleeding. While there was a potential survival benefit during the first years after surgery for patients receiving a biological valves the difference became insignificant after a follow-up of 10 years. Electronic supplementary material The online version of this article (10.1186/s13019-019-0943-6) contains supplementary material, which is available to authorized users.