European wild rabbits (Oryctolagus cuniculus) are frequently translocated for hunting and conservation purposes. Quarantining these animals prior to release reduces the risk of releasing rabbits incubating field infections of myxomatosis or viral haemorrhagic disease (RHD), and it provides a way to vaccinate these animals against both diseases. However the optimal quarantine period needed to achieve these goals is not known. We therefore assessed the effects of quarantine lengths (2, 4, 6, 8 weeks) on rabbit biochemical parameters, immunity induced by vaccination against myxomatosis and RHD, and survival of translocated rabbits. We found that levels of total bilirubin, urea nitrogen, aspartate aminotransferase (AST), and alanine aminotransferase (ALT) enzymatic activities were significantly (P < 0.05) decreased during quarantine, independent of quarantine length, whereas hematocrit levels increased significantly. All pregnant female rabbits aborted or lost litters during quarantine. Seroconversion against myxomatosis and RHD following vaccination was not related to any biochemical parameter at vaccination time, but the proportion of seronegative rabbits that seroconverted was moderate. The heterophil/lymphocyte ratio, conjugated to unconjugated bilirubin ratio, and the serum AST and creatinine levels we measured after capture and transport were directly related to mortality through the quarantine period, whereas we found total serum protein level was negatively related to mortality. Mortality after release was positively related to urea nitrogen concentration and negatively related to hematocrit and the albumin/globulin ratio, but it was independent of quarantine length. Based on our findings, rabbit translocation programs that include a quarantine period could be improved by decreasing the acute stress induced by capture and handling prior to quarantine; facilitating a more rapid access to high quality feed during quarantine; and improving the vaccination protocol. In addition, the release from quarantine of rabbits should be determined by their physical condition, not merely by elapsed time in quarantine.