Infectious diseases impair Se metabolism, and low Se status is associated with mortality risk in adults with critical disease. The Se status of neonates is poorly characterised, and a potential impact of connatal infection is unknown. We hypothesised that an infection negatively affects the Se status of neonates. We conducted an observational case-control study at three intensive care units at the Charité-Universitätsmedizin Berlin, Germany. Plasma samples were collected from forty-four neonates. On the basis of clinical signs for bacterial infection and concentrations of IL-6 or C-reactive protein, neonates were classified into control (n 23) and infected (n 21) groups. Plasma Se and selenoprotein P (SePP) concentrations were determined by X-ray fluorescence and ELISA, respectively, at day of birth (day 1) and 48 h later (day 3). Se and SePP showed a positive correlation in both groups of neonates. Se concentrations indicative of Se deficit in adults (<20 µg/l) were observed in four infected neonates and one control subject, and three infected neonates had very low SePP concentrations (<0·5 mg/l). The univariate analysis revealed a significant difference in Se and SePP concentrations between the groups. Both parameters correlated inversely to IL-6 in neonates with severe inflammation (IL-6 >500 ng/l). During antibiotic therapy, SePP increased significantly from day 1 (1·03 (SD 0·10) mg/l) to day 3 (1·34 (SD 0·10) mg/l), indicative of improved hepatic Se metabolism. We conclude that both Se and SePP are suitable biomarkers for assessing Se status in neonates and for identifying subjects at risk of deficiency.