Reports of congenital chondrodystrophy of unknown origin (CCUO) have been anecdotally associated with periods of drought during the gestation period of affected beef calves. Reported sporadically in the past, the incidence of CCUO has increased in south-eastern Australia and has been reported every year between 2002 and 2007. A maternal nutritional deficiency arising from poor quality pastures and supplements has been suggested as contributing to the disorder. With an increase in drought occurrence predicted by climate change models, it is possible that the incidence will increase into the future. Retrospective data collected during a case control study was used to determine if the occurrence of cases of CCUO was associated with rainfall deficiency during gestation. A total of 799 cases occurring on 46 farms in south-eastern Australia were identified and a time series of cases was created. The association of both average monthly and three-month average rainfall with cases of CCUO revealed a significant negative correlation (r=-0.29 and r=-0.37 respectively, P<0.05) five months prior to the birth of CCUO calves on the farms studied. Logistic regression analysis showed a 3.3 (CI 1.8; 5.8, P<0.001) times increased risk of CCUO calves when the three-month average rainfall was in the lowest decile five months prior to the birth of calves. This information may be used to alert farmers as to when high quality supplemental feed may be provided to improve maternal nutrition and reduce the number of CCUO calves born.