Objective: The aim of the study was to compare C-reactive protein (CRP), procalcitonin (PCT) and serum amyloid A (SAA) levels in children with bacterial infection. Material and Methods: In this prospective study, 120 pediatric patients who were hospitalized with bacterial infection in the Uludag University Medical Faculty Pediatric Clinic between June 2009 and June 2011 were included. Patients were evaluated in 5 groups as sepsis, pneumonia, meningitis, pyelonephritis and other infection groups. Before initiating the antimicrobial therapy, blood samples for whole blood count, blood culture, CRP, PCT and SAA were obtained from children with bacterial infection. This procedure was repeated three times at 48 h, 7 and 10 days. Whole blood count was performed using an automated counter, Cell Dyn 3700 (Abbott Diagnostics Division, Santa Clara, CA, USA). CRP and SAA were determined by an immunonephelometric method using BN II device (Dade Behring Marburg GMBH, Marburg, Germany). PCT was measured by Enzyme- Linked Fluorescent Assay (VIDAS PCT; Brahm Diagnostica GMBH, Lyon, France). Results: Of the patients, 66 (55%) were male and 54 (45%) were female. The median age was 37.5 months (1-209). PCT levels of the sepsis group was significantly higher than those of the pneumonia and other infection groups (respectively, p=0.001, p=0.003). SAA levels were higher in the meningitis group than those of the pneumonia group (p=0.007). When patients were divided into two groups as invasive bacterial infection group and localised bacterial infection group; PCT levels were found significantly higher in the invasive bacterial infection group than those of the localised bacterial infection group. Also, percentage change of PCT at the 48th hour, 7 and 10 days was determined as significantly higher in the invasive bacterial infection group than that of the localised bacterial infection group. Conclusion: In this study, PCT seems to be a more valuable parameter in diagnosing invasive bacterial infections. © 2013 by Pediatric Infectious Diseases Society.