Objective: The aim of this study was to compare cord blood S100B levels and cord blood gas parameters of term infants with meconium-stained amniotic fluid (MSAF) to those infants with clear amniotic fluid. Methods: Term pregnant women at an active phase of labor and having MSAF were defined as the study group (n = 35) and pregnant women with clear amniotic fluid, and matched for age, parity, and gestational age were defined as the control group (n = 35). Cord blood S100B levels and gas parameters were measured. Results: LogS100B values of study and control groups were 2.40 +/- 0.21 and 2.43 +/- 0.29 pg/ml, respectively. The difference was not statistically significant (p = 0.675). LogS100B levels slightly increased as meconium thickened. (2.32 +/- 0.16, 2.41 +/- 0.17, and 2.44 +/- 0.28 pg/ml, respectively). However, no difference was found between groups (p = 0.438). Moreover, the study group had a statistically lower HCO3 level (21.80 vs 23.60 mmol/l) and a higher rate of base deficit (4.85 vs 3.25 mmol/l) than the control group. However, median HCO3 and base deficit values were within normal limits in both groups. Conclusion: The present study showed that cord blood S100B levels of infants born through MSAF were not different from those with clear amniotic fluid. This finding suggests that MSAF, regardless of its thickness, may not be related to brain damage in low risk term pregnancies.