OBJECTIVE An analysis of occurrence of selected birth defects in the Czech Republic in 2006. Comparison of mean incidences of selected birth defects during the 1994-2006 to previous period data. METHODS Retrospective epidemiological analysis of birth defects incidences from the Czech National Birth Defects Register database. METHODS Data from the National Birth Defects Register (Institute for Health Information and Statistics) in the Czech Republic in the 1994-2006 period were used along with data on prenatally diagnosed and terminated pregnancies from the same period. Mean incidences of selected types of defects (anencephaly, spina bifida, encephalocele, total neural tube defects, congenital hydrocephalus, omfalocele, gastroschisis, total abdominal wall defects, diaphragmatic hernia, renal agenesis/hypoplasia, cystic kidney, Down syndrome and others) in 2006 were analyzed. For a retrospective analysis, already published data on birth defects in the Czech Republic were used. RESULTS During 1961-2006 period, totally 6,173,629 children were born on the area of the Czech Republic, out of which almost 105,000 with a birth defect. Mean incidence was 170 per 10,000 live births. In 1994-2006, totally 1,238,398 children were born, out of which more than 42,000 with a birth defect. Mean incidence was 339 per 10,000 live births (with highest value of 414.58 in 2003). In 1994-2006, 6113 cases of prenatally detected birth defects (resulting in pregnancy termination) were registered, in relative numbers 49.3 per 10,000 live births (2006 63.3 per 10,000). During 1961-2006, totally 2028 anencephaly, 2647 spina bifida, 462 encephalocele, 5137 total neural tube defects, 3904 congenital hydrocefalus, 1627 omfalocele, 941 gastroschisis, 2568 total abdominal wall defects, 1754 cystic kidney, 1475 renal agenesis/hypoplasia, 1442 diafragmatic hernia, 6328 Down syndrome, 994 oesophageal defects, 1670 anorectal malformations, 6856 cleft lip and/or palate and 4440 cleft palate cases were registered. Current incidences for 2006 and mean incidences for the 1961-2006 period (in brackets), both per 10,000 live births were as follows: anencephaly 2.17 (3.34), spina bifida 4.82 (4.36), encephalocele 1.23 (0.76), total neural tube defects 8.22 (8.47), congenital hydrocefalus 3.78 (6.43), omfalocele 3.12 (2.68), gastroschisis 2.46 (1.55), total abdominal wall defects 5.57 (4.23), cystic kidney 8.98 (2.89), renal agenesis/hypoplasia 8.60 (2.43), diafragmatic hernia 3.78 (2.38), Down syndrome 20.32 (10.43), oesophageal defects 1.56 (1.61), anorectal malformations 2.54 (2.71), cleft lip and/or palate 5.47 (11.11) and cleft palate 7.42 (7.19). CONCLUSIONS The study gives updated results of incidences analysis of both pre- and postnatally diagnosed birth defects in the Czech Republic until 2006. Some birth defect incidences in live birth are decreasing recently (neural tube defects, abdominal wall defects, Down syndrome), some are increasing (oesophageal defects, anorectal malformations). Some incidences in births are influenced by an increased efficiency of diagnostics (renal defects) some remain more or less on the same level (diaphragmatic hernia) or just oscillate (facial defects).