An imbalance between the coagulation and fibrinolysis can be observed at the initial phase of bacterial infection, where an essential role is played by antithrombin III (AT III) and protein C (PC). The aim of the current study was to determine relationship between antithrombin III and protein C in prognosis of neonatal sepsis and evaluate diagnostic value of these parameters. The study included 330 new-borns, hospitalized at the Neonatal Department of the Jagiellonian University in Cracow. The first group consisted of 150 new-borns (age 1 to 7 days) diagnosed as congenital infections. The second group consisted of 150 new-borns, in whom clinical signs of infection appeared after the 7th day of life. The third group (control) comprised 30 healthy, mature new-borns. The sepsis was diagnosed based on the following laboratory results: blood cell count, procalcitonin, C-reactive protein and interleukin-6 blood plasma concentration. Depending on coexisted clinical signs: urine, cerebrospinal fluid or BAL lavage were examined bacteriologically. In each child, activity of AT m and PC serum level was measured. In the control group only activity of AT III and PC were measured. In conclusion, based on obtained results we found that AT III and PC may be valuable diagnostic markers of haemostasis disorders observed in early phase of sepsis. Worth to notice is an observation that low level ( ; < 10%) of PC is indicative for high risk of death, thus the supplementation of this protein seems to be essential for the therapy of sepsis in neonates with initial PC depletion. Such statement can't be proved for AT m supplementation.