OBJECTIVE An analysis of birth defects occurrence in the Czech Republic in 2004 and a comparison to data from 1996-2003. TYPE OF STUDY A retrospective analysis of data from a National Register of Congenital Anomalies of the Czech Republic. METHODOLOGY Data on birth defects in the Czech Republic from the Institute of Health Information and Statistics--National Register of Congenital Anomalies from the 1996-2004 period were used. An analysis of incidence of selected type of birth defects was performed along with their contribution to perinatal mortality according to particular types of defects. RESULTS There were 29 186 children born with a birth defect, out of it were 17,063 boys and 12,116 girls, an undetermined sex was reported in 7 cases. A mean incidence of birth defects 2004 in was 367.9/10,000 live births. Corresponding data from years 2003, 2002 and 2001 were 405.2, 4043 and 407.9/10,000 live births. CONCLUSIONS Current data on birth defects in 2004 in the Czech Republic are presented with a comparison to a 8-year period. An analysis of temporal and demographic changes in birth defects incidence is given along with data on birth defects contribution to perinatal mortality in selected types of defects.