Between 1989 and 1997, 8204 rough collies were examined for collie eye anomaly (CEA) at up to 10 weeks of age. All dogs were positively identified and the results were registered under the Swedish Kennel Club genetic health programme. A significant decrease in litter size occurred if one of two affected parents had coloboma (3.8 pups) compared with litters from two chorioretinal dysplasia- (CRD-) affected collies (5.2 pups) or litters by two normal collies (5.0 pups), indicating an influence of the coloboma genotype on offspring vitality. The prevalence of CRD in pups from normal x normal matings and CRD x CRD matings was significantly different from that expected under simple autosomal recessive inheritance (43 per cent versus 25 per cent and 85 per cent versus 100 per cent). The results are compatible with polygenic inheritance but not with simple autosomal recessive inheritance. CRD prevalence in offspring of CRD x coloboma matings was significantly lower than in pups of CRD x CRD matings, reflecting effects of the coloboma genotype on vitality. These results have important implications for breeding programmes and the genetic control of CEA.