The capture and handling of live European wild rabbits (Oryctolagus cuniculus) are unavoidable initial steps for immunization by vaccination against viral hemorrhagic disease (VHD) and myxomatosis as a management tool aimed at enhancing wild rabbit populations. We investigated the short-term effects of vaccination campaigns against VHD and myxomatosis on the survival of 206 European wild rabbits in a Spanish population. While no effect was observed on the survival of adult rabbits, young and subadult rabbits (P < 0.001) had higher mortality rates during the first week after handling than in the subsequent 3 weeks. The hazard rate of death from disease was inversely correlated with body condition (P < 0.001) during the first week. Vaccination increased the hazard rate of death due to disease during the first 7 days post-handling, although this detrimental effect was higher in young rabbits (P = 0.012) and modulated by body condition (P = 0.004). The hazard rate of dying from predation during the first week was higher for males than females (P = 0.023) and in subadults compared to young rabbits (P = 0.004). Body condition was inversely related to the predation hazard rate (P = 0.002). Our results suggest that vaccination campaigns had a short-term negative impact caused by the stress of handling in addition to the detrimental effects of vaccination against VHD and myxomatosis. Future studies should consider this negative impact to assess the true efficacy of vaccination campaigns in wild populations.