Infection is a leading cause of neonatal morbidity and mortality worldwide. Premature neonates are particularly susceptible to infection because of physiologic immaturity, comorbidity and extraneous medical interventions. Additionally, premature infants are at higher risk of progression to sepsis or severe sepsis, adverse outcomes and antimicrobial toxicity. Currently, initial diagnosis is based upon clinical suspicion accompanied by non-specific clinical signs, and is confirmed upon positive microbiologic culture results several days after institution of empiric therapy. There exists a significant need for rapid, objective, in vitro tests for diagnosis of infection in neonates who are experiencing clinical instability. We used immunoassays multiplexed on microarrays to identify differentially expressed serum proteins in clinically infected and non-infected neonates. Immunoassay arrays were effective for measurement of more than 100 cytokines in small volumes of serum available from neonates. Our analyses revealed significant alterations in levels of eight serum proteins in infected neonates, which are associated with inflammation, coagulation, and fibrinolysis. Specifically, P- and E-selectins, Interleukin 2 soluble receptor alpha, Interleukin 18, Neutrophil Elastase, urokinase Plasminogen Activator and its cognate receptor, and C reactive protein were observed at statistically significant increased levels. Multivariate classifiers based on combinations of serum analytes exhibited better diagnostic specificity and sensitivity than single analytes. Multiplexed immunoassays of serum cytokines may have clinical utility as an adjunct for rapid diagnosis of infection and differentiation of etiologic agent in neonates with clinical decompensation.