To evaluate the effect of single oral dose of 50 mg/kg clofibrate in hyperbilirubinemia of term healthy neonates in Yazd, Iran. A parallel single- blinded randomized clinical trial, conducted on 60 healthy term neonates admitted between July and December 2007 to Shahid Sadoughi Hospital. Inclusion criteria were neonates with gestation age of 38-42 wk, birth weight of 2500-4000 g, product of normal vaginal delivery, breast-fed and total serum bilirubin (TSB) level of 17-29.9 mg/dL. Neonates with sepsis, anemia, severe asphyxia, hemolytic diseases, major congenital anomalies, indirect hyperbilirubinemia and underlying hepatic disorders were excluded. Selection of patients was based on random allocation via table of random numbers and the patients distributed into two groups. In group one, 30 neonates were treated with phototherapy alone and in 30 of other group treatment done with single dose of 50 mg/kg clofibrate and phototherapy. The primary endpoint with respect to efficacy in reducing of TSB was achieving TSB to less than 14 mg/dL as measured at the beginning, 12, 24 and 48 h after the start of phototherapy. Secondary outcomes were hospital stay days, duration of phototherapy and side effects of treatments during hospital stay and on the second day after discharge. No significant differences were seen from the viewpoint of rout of delivery, gender, gestational age, birth weight, hemoglobin and bilirubin level at time of admission and weight in discharge time in the two groups. After 48 h of intervention, 27 (90%) neonates in clofibrate group and 15 (56.7%) in control group had TSB of less than 14 mg/dL (p 0.02). Mean TSB 12 h after treatment (mean ± SD: 14.82 ± 1.7 mg/dL vs. 16.67 ± 1.77 mg/dL, P 0.001), 24 h after treatment (mean ± SD: 11.97 ± 2.92 mg/dL vs. 14.61 ± 2.52 mg/dL, P 0.001) and 48 h after treatment (mean ± SD: 7.91 ± 2.45 mg/dL vs. 12.74 ± 2.21 mg/dL, P 0.0001), mean of hospital stay days (mean ± SD: 1.7 ± 0.7 days vs. 3.2 ± 1.2 days, P 0.03) and duration of phototherapy (mean ± SD: 30.2 ± 13.99 h vs. 46.2 ± 15.58 h, P 0.001] were significantly lower in clofibrate group. Only loose stool was seen in two patients of clofibrate group and no significant difference was seen from view of safety of the treatments. A single dose of 50 mg/kg clofibrate in treatment of neonatal hyperbilirubinemia is effective, safe and cost effective in view of reducing hospital stay days.