We describe the secular trend, pattern and causes of congenital anomalies (CAs) in the Pleven region, Bulgaria. The source of the data was the regional population-based registry of CAs using criteria according to EUROCAT recommendations. During the period 1988-2006, 47,622 births were surveyed. A total of 1,225 cases of CAs were ascertained, giving a total prevalence of 25.72 [95% confidence interval (95% CI) 24.3 to 27.15 per 1,000 births. There was a significant increase in total prevalence from 17.76 per 1,000 births in 1988 to 29.40 in 2006 (c2 test for trend = 5.03; p = 0.025). Congenital heart disease (4.3 per 1,000 registered births), nervous system anomalies (3.3 per 1,000 births), limb defects (2.5 per 1,000 births) and neural tube defects (2.0 per 1,000 births) demonstrated the highest prevalence. There was a significant upward trend in the prevalence of some specific anomalies: digestive system, tumors, gastroschisis and non syndromal dysmorphologic conditions. Genetic causes were identified in approximately 62% of all cases with CAs (chromosomal 8%, single gene defects 14%, multifactorial 40%). The secular trend and particular pattern of CAs in the Pleven region require some potential underlying contributing factors to be considered: case ascertainment and diagnostic methods, and some environmental factors. These data draw attention to the need of further regional epidemiological studies. The high proportion of genetic causes emphasize the role of genetic services as an integral part of preventive medical care.