SummaryBackgroundAllogeneic mesenchymal stem cells (MSCs) are a promising cell source for treating musculoskeletal injuries in horses. Controversy exists, however, over whether major histocompatibility complex (MHC)‐mismatched MSCs are recognised by the recipient immune system and targeted for death by a cytotoxic antibody response.ObjectivesTo determine if cytotoxic anti‐MHC antibodies generated in vivo following MHC‐mismatched MSC injections are capable of initiating complement‐dependent cytotoxicity of MSCs.Study designExperimental controlled study.MethodsAntisera previously collected at Days 0, 7, 14 and 21 post‐injection from 4 horses injected with donor MHC‐mismatched equine leucocyte antigen (ELA)‐A2 haplotype MSCs and one control horse injected with donor MHC‐matched ELA‐A2 MSCs were utilised in this study. Antisera were incubated with ELA‐A2 MSCs before adding complement in microcytotoxicity assays and cell death was analysed via eosin dye exclusion. ELA‐A2 peripheral blood leucocytes (PBLs) were used in the assays as a positive control.ResultsAntisera from all 4 horses injected with MHC‐mismatched MSCs contained antibodies that caused the death of ELA‐A2 haplotype MSCs in the microcytotoxicity assays. In 2 of the 4 horses, antibodies were present as early as Day 7 post‐injection. MSC death was consistently equivalent to that of ELA‐A2 haplotype PBL death at all time points and antisera dilutions. Antisera from the control horse that was injected with MHC‐matched MSCs did not contain cytotoxic ELA‐A2 antibodies at any of the time points examined.Main limitationsThis study examined MSC death in vitro only and utilized antisera from a small number of horses.ConclusionsThe cytotoxic antibody response induced in recipient horses following injection with donor MHC‐mismatched MSCs is capable of killing donor MSCs in vitro. These results suggest that the use of allogeneic MHC‐mismatched MSCs must be cautioned against, not only for potential adverse events, but also for reduced therapeutic efficacy due to targeted MSC death.