To describe the epidemiology of congenital anomalies in Glasgow with special reference to secular trends. The prevalence of congenital anomalies was determined retrospectively in 233 777 births using the Glasgow Register of Congenital Anomalies for the period 1980-97. The total prevalence of congenital anomalies was 324 per 10 000 births, declining by just over a third from 382 per 10 000 births in 1980 to 238 per 10 000 births in 1997. The categories of defects with the highest prevalence were congenital heart disease (50 per 10 000 births), anomalies of limbs (49 per 10 000 births), and digestive system anomalies (47 per 10 000 births). Prevalence in most categories of anomaly declined, including those of the ear (-88%), congenital heart disease (-69%), anomalies of integument (-67%), nervous system anomalies (-61%), anomalies of limb (-54%), and urogenital (including renal) anomalies (-31%). By contrast, there was a significant upward trend for chromosomal anomalies (+50%). Despite the decline in the prevalence of many types of congenital anomaly, around 2.5% of all births in Glasgow were still associated with these disorders in 1997. In attempting to explain the prevalence and secular trend of congenital anomalies in Glasgow, underlying contributing factors require to be considered. These include changes in case ascertainment, antenatal screening, and diagnostic methods.