A previous study reported that the incidence of hyponatremia after linezolid (LZD) use was higher than that with vancomycin (VCM) use in adults. However, hyponatremia due to LZD in neonates and infants was not investigated. This study aimed to compare the incidence of hyponatremia between LZD and VCM use in neonates and infants.The retrospective study was conducted at the Aichi Medical University Hospital. All patients who were cared for in NICU or GCU and received ≥3 days of LZD or VCM were included in this study. Hyponatremia was defined as serum sodium level ≤134 mEq/L and ≥5 % decrease from baseline after administration of LZD or VCM.A total of 76 patients (LZD, N = 36; VCM, N = 37) were included. There was no significant difference in the incidence of hyponatremia between the two groups (19.4 % vs 16.2 %, p = 0.72). The proportion of patients with a minimum value of serum sodium ≤134 mEq/L during treatment was 47.3 % in the LZD group and 35.1 % in the VCM group (p = 0.29), and the decrease in serum sodium level from baseline to the minimum value was 80.5 % and 78.4 %, respectively (p = 0.85).In conclusion, there was no significant difference in the incidence of hyponatremia between the LZD and VCM groups. Therefore, it is not necessary to avoid LZD use in neonates and infants because of the risk of hyponatremia.