A recently developed method to quantitate prothrombin in plasma uses the carinactivase-1 (CA-1) method. The present study was designed to establish the reference value by the CA-1 method in the neonatal period and to explore the effect of gestational age, birth weight, concurrent diseases, and vitamin K administration on the prothrombin levels. We enrolled 78 consecutive neonates. The gestational ages ranged from 28 to 41 weeks, and the birth weight ranged from 850 to 3750 g. Twenty-nine infants had concurrent diseases, and the others (n = 49) were healthy. A 300 muL blood sample was drawn into a plastic syringe containing 60 U freeze-dried buffered heparin. Prothrombin levels did not differ between appropriate-for-date (AFD) and light-for-date (LFD) babies (p = 0.090) or between groups with and without concurrent diseases (p = 0.210). In healthy AFD babies, prothrombin levels correlated with gestational age (r = 0.465, p = 0.003) and birth weight (r = 0.458, p = 0.003). In healthy low-birth-weight infants (n = 14) and those with concurrent diseases (n = 17), the changes after vitamin K administration were not significant. The CA-1 method is of clinical use in monitoring coagulation during the early neonatal period.