Background: Precise and quick diagnosis of jaundice in the neonates is of major medical and economic importance. Biomarkers in serum are regularly applied in clinical settings. Nevertheless, saliva could be a substitute to assess biomarkers. In this study, we aimed to detect the probable association between salivary and serum levels of bilirubin in jaundiced neonates. Methods: A case-control survey was performed on 30 healthy neonates and 30 neonates with jaundice hospitalized in Mirzakhochekkhan and Baharloo hospitals, Tehran, Iran. Bilirubin levels were assayed in serum and unstimulated whole saliva by a photometric method. Pearson correlation and Student's t tests were used for statistical analysis. Results: The mean salivary and serum levels of total bilirubin were significantly higher in the neonates with jaundice compared to healthy individuals. A moderate correlation was observed between serum and salivary concentrations of total bilirubin. Conclusions: Serum and salivary levels of bilirubin are meaningfully correlated in jaundiced neonates. This correlation may facilitate the monitoring and evaluation of bilirubin levels non-invasively for jaundice.