The Victorian Birth Defects Register (VBDR) is a population-based surveillance system with a primary function of monitoring trends in birth defects. This paper outlines the processes undertaken in Victoria, Australia, to obtain population prevalence rates of birth defects and investigates the effect on the prevalence rates of variations in collection and processing tasks. It includes all birth defects that were notified to the VBDR by 31 December 2004. The overall prevalence rate of birth defects in Victoria for 2003 was 4.0%, with an overall accuracy rate of 88%. However, this proportion varied according to what birth defects were included, the age by which birth defects were diagnosed, changes to sources of ascertainment, inclusion of terminations of pregnancy, or reporting by cases rate (infants affected) or birth defect rate (individual birth defects). Taking all of these factors into consideration, we are confident that 4.0% is an accurate population prevalence rate of birth defects in Victoria for 2003.