The aim of this study was to analyze the acute phase protein response during early onset (<72 h) neonatal sepsis by high-resolution two-dimensional electrophoresis (2-D PAGE). Cord and serial plasma/serum samples from eight neonates with sepsis (positive blood culture) were examined(gestational age, median 33.5 weeks; range 24.3-40.6, pre-term: n=4 full term: n=4; birth-weight, median 2,635 g; range 600-3,400; onset at birth, n=6; at 7.5 h, n=1; at 48h, n=1). Isolated microorganisms were: S. agalactiae (n=4/8), C. striatum (n=2/1. 8), L. monocytogenes (n=1/8) and C. albicans (n=1/8). Admission to the Neonatal Intensive Care Unit was necessary for 7 infants (hospitalization time, median 22.5 days, range 5-82). Clinical outcome was favorable in 7 cases, lethal in one. Plasma/serum samples from five gestational age- and sex-matched control infants (repeated negative blood cultures; absent histological chorioamniositis and clinical symptoms) were also analyzed. 2D-PAGE was performed using an immobiline polyacrylamide system. Routine sample load was 0.75 μl. Isoelectric focusing was carried out on non-linear wide-range immobilized pH (3-10) gradients. The second dimension was performed on 9-16% SDS-PAGE linear gradient gels. Silver-stained gels were scanned with a computing densitometer. Image analysis and on-line matching were carried out using MELANIE II software (Biorad). Haptoglobin (Hpt) (n=8/8) and serum amyloid A protein (SAA)(n=5/8;term infants 4/4, pre-term 1/4) in cord blood were significantly correlated with sepsis, though they were absent among controls (p<0.001). Hpt and SAA spots were identified in silver-stained electrophoretograms, confirmed by immunoblotting with specific antibodies. Hptβ-chains appeared to be under-sialylated in pre-term infants, while post-translation modifications of α-chains and SAA were similar to those observed in the adult. Different Hpt α-chain phenotypes than those in maternal serum were observed, indicating that cord blood Hpt originates from neonatal synthesis. Inconsistent changes in typical acute phase proteins(α1-antitrypsin, α1-antichymotrypsin, leucine-richα2-glycoprotein, α2-HS glycoprotein, transthyretin and serum retinol-binding protein) were present. The findings indicate that the acute phase protein response in the newborn: 1) differs from those of other periods in life in that is limited to changes in Hpt and SAA; 2) is gestational age-dependent. Finally, the data suggest that cord blood Hpt and SAA may be potentially useful early markers for neonatal sepsis.