Objective Positive CSF culture is the gold standard for the diagnosis of meningitis but it carries poor sensitivity. CSF procalcitonin (PCT) is shown to have some utility for the diagnosis of meningitis though there are limited studies in neonatal age group. We planned this study to compare CSF, serum, and CSF to serum PCT levels in neonates with confirmed, probable, and nonmeningitis groups to determine its optimal cut-off in CSF and serum for diagnosing meningitis Study Design Sixty-seven neonates who qualified for lumbar puncture were enrolled in the study. Neonates were categorized into confirmed meningitis, i.e., CSF cytochemistry and culture positive (N = 17), probable meningitis, i.e., CSF cytochemistry positive but culture negative (N = 25) and nonmeningitis, i.e., both cytochemistry and culture negative (N = 25). CSF and serum samples were stored at −80°C for PCT assay. Results Significant difference was seen in mean of CSF PCT in neonates with confirmed (0.31 ng/mL), probable (0.22 ng/mL), and nonmeningitis (0.11 ng/mL) groups. Similarly, significant difference was observed in serum PCT levels also, though the ratio of serum to CSF PCT was comparable. At cut-off of 0.2 ng/mL, CSF PCT had sensitivity of 95.2% and specificity of 96% in the diagnosis of meningitis. Conclusion CSF PCT is more specific marker for the diagnosis of neonatal meningitis as compared with serum PCT and CSF to serum PCT ratio. Key Points