Serum lactate concentration provides clinically important information on metabolic status of critically ill neonates. Aim The purpose of the study was to assess some factors influencing lactate levels during first 48 h of intensive treatment. Setting A university hospital pediatric intensive care unit (PICU). Methods 173 neonates (gestational age 35 hbd /median/, mean birth weight 2045 ± 808 g, SNAP score -9 /median/) subsequently admitted to PICU in first two days of life were studied. Blood lactate levels, blood gases, electrolytes and glucose levels were determined at the admission and after 24 and 48 h of PICU treatment. SNAP score and data concerning oxygen transport into the tissues were collected simultaneously. Results Blood lactate levels increased with low mean arterial pressure (P < 0.001), low Apgar score (at 5 min), P < 0.01 at admission, P < 0.05 in 24 h, ns in 48 h, low temperature at admission, P < 0.001, low hematocrite P < 0.05 and high SNAP value, P < 0.001. No significant correlations between lactates and other demographic and clinical data were observed. Conclusions Based on our results we conclude that hypoperfusion and bad clinical condition (SNAP score) has the strongest impact on blood lactates. Of interest we found persistent effect of asphyxia evaluated as Apgar score and hypothermia at the admission on high lactate incidence.