This study examined the risk of congenital anomalies in infants born in South Australia to women with maternal diabetes in a population-based cohort study of births over a 15-year period, 1986-2000. Differences in the reporting, recording, and diagnosis of pre-existing diabetes mellitus, gestational diabetes mellitus, and impaired glucose tolerance make comparisons between studies difficult. In order to compare published research, details of research methods and analytic approaches are required to understand the potential confounding, bias, and effect modification that may occur. Data on congenital anomalies from the South Australian Birth Defects Register were linked to birth data from the Pregnancy Outcome Statistics Unit of the South Australian Department of Health. This enabled information on congenital anomalies to be linked to pregnancy details, including diabetes status. Between 1986 and 2000, the prevalence of congenital anomalies in the infants of mothers with pre-existing diabetes mellitus, gestational diabetes mellitus, or impaired glucose tolerance was significantly higher than in the total population; relative risk = 2.01 (1.66-2.43) and 1.19 (1.08-1.31), respectively. This increased prevalence was not modified by adjustments for maternal age, ethnicity, or other demographic factors, nor did the rate change over the 15 years of the study period. The prevalence of congenital anomalies was found to be significantly higher in the infants of mothers with maternal diabetes. Larger population-based studies are needed to determine which anomalies are involved and how their occurrence can be reduced. Birth Defects Research (Part A), 2005. (c) 2005 Wiley-Liss, Inc.