Since 1956, when the Basle Zoo (Switzerland) initiated the breeding of lesser kudu (Tragelaphus imberbis), 43% of the lesser kudu juveniles died before reaching an age of 6 mo. In this study, the objective was to obtain the pathological findings, nutritional history, and family tree information in order to evaluate the influence of husbandry on juvenile mortality in these animals. The main cause of death was white muscle disease (WMD), diagnosed in 14 cases (26%) of the deceased juveniles. Although enclosure size had remained constant and animal accessibility to the public was constantly high, both herd size and juvenile mortality had increased from 1956–2004. The diet consumed by the whole group in 2004 had deficient levels of vitamin E and selenium. The increasing linear trend of the mortality rate since the 1960s was significant, and there was a significant correlation between herd size and overall juvenile mortality. In contrast, there was no correlation between herd size and the occurrence of juvenile mortality associated specifically with WMD. Other investigated factors (sex, inbreeding, and season) had no significant effect on overall mortality up to 6 mo of age or on mortality associated with WMD. These results characterize both a dietary and a husbandry problem, and are supported by a lack of similar juvenile mortality in another facility where the diet was supplemented with vitamin E, animal numbers were kept low, and the enclosure structure offered more retreat options for the animals.