OBJECTIVE To evaluate neonatal mortality rate (NMR) in 1998 and 1999 years in the Czech Republic. METHODS Retrospective epidemiological study of all alive newborns born in 1998 and 1999 in the Czech Republic. METHODS 12 perinatological centers of nine regions of Bohemia and Moravia. METHODS All alive, died, died with congenital defects newborns were registered and results of neonatal mortality rate and specific neonatal mortality rate were calculated. The main causes of death were divided into four groups (intraventricular hemorrhage grade III-IV, infection, acute respiratory failure and others) and evaluated comparatively. In 1999 the NMR of newborns with birth weight below 500 g and their survival were introduced for the first time in the Czech Republic. RESULTS The fluent decrease of NMR during nineties was stopped in 1999. Increase of NMR from 2.8@1000 in 1998 to 3.0@1000 in 1999 was mainly caused by arise of specific neonatal mortality rate in newborns weighing > or = 2000 g. Comparing 1998 and 1999 years, two times more these newborns without serious congenital defects died in 1999 (28 vs. 56). Specific neonatal mortality rate of extremely low birth weight newborns further decreased (359@1000 vs. 279@1000) especially in the newborns with birth weight between 500-749 g (543@1000 vs. 373@1000). The most frequent main causes of death still has been intraventicular haemorrhage grade III-IV and infection in very low birth weight newborns, and serious congenital defects and infection in newborns weighing > or = 1500 g. The concentration of very low birth weight newborns to perinatological centers by transfer in uterus was 81% in 1998 and 83% in 1999. The differences in neonatal mortality rates between nine regions of Bohemia and Moravia has been getting equal but has been still great in specific neonatal mortality rate of extremely low birth weight newborns between the best and worst regions (147@1000 vs. 458@1000). There were registered 19 newborns weighing < or = 500 g surviving more than 24 hours after delivery in the Czech republic. Specific neonatal mortality rate of these newborns was 316@1000 and 527@1000 survived. CONCLUSIONS Reserves for further lowering of NMR are improving the care after extremely low birth weight newborns in the regions with below average results and decreasing the mortality of newborns with birth weight > or = 2000 g by introducing of group B streptococcus prophylaxis, improving prenatal diagnostics of serious congenital defects and early and more quality postnatal transport of newborns suffered from acute respiratory failure to centers disposing of the latest methods of treatment.