A case-control study was conducted on 46 farms in south-eastern Australia with a recent history of congenital chondrodystrophy of unknown origin (CCUO) between 2002 and 2007. For each farm data was collected using face-to-face interviews concerning the management of case and control mobs during the gestation period in which affected calves were born. Data concerning the paddocks in which gestating cattle were maintained was also collected for analysis. Three separate multivariable models were constructed using generalised linear mixed models (GLMMs). The first model was based on the dichotomous outcome of mob status (affected/not affected) and included explanatory variables for management and environment factors. The second model used a novel approach, taking into account the number of cases in affected mobs in order to utilise available data. The outcome events/trials was used where the numerator was equal to the number of affected calves in a mob, and the denominator was equal to the total number of calves in the mob. The third model used the dichotomous outcome paddock status and included environmental and soil variables for paddocks involved with case and control mobs. Confounding for dam age and year affected was included in the mob outcome models, and random effects for paddock and farm were incorporated into the models. The birth of CCUO calves was associated with dams grazing native pastures on hilly terrain during gestation. Low levels of pasture were also associated with the outcome. The two models used for the mob outcome were similar in many respects. The events/trial model included the use of supplemental feed and an interaction term. This study demonstrates an association between a maternal nutritional disturbance and the occurrence of CCUO.