Background Most children in low-income countries have inadequate dietary zinc. The study was aimed to demonstrate the effect of iron-zinc fortified milk in improving zinc status among underweight school children in Indonesia. Objective To evaluate the effects of milk fortification with zinc on serum zinc levels in underweight Indonesian school children. Methods A double-blind, randomized, controlled, communitybased study was conducted on 426 underweight children aged 7 to 9 years in several low economic income level elementary schools in Jakarta and Solo. Subjects were randomly allocated to receive either zinc-fortified milk (n= 217) or standard milk (n=209) for 6 months. The fortified milk provided an 2.38 mg zinc per day and the standard milk provided 0.88 mg zinc per day. Results Among underweight children, the prevalence of stunting with a height-for-age z-score < - 2.0 SD was 39.7%. Almost all subjects (98%) had zinc intake ofless than 60% of the Indonesian recommended daily allowance (RDA) for that particular age group. After receiving the milk intervention, mean serum zinc concentration declined significantly in both groups (from 13 .50 ±3.05 μmol/Lat baseline to 10.59±1.93 μmol/L, P< 0.05), but growth parameters (weight and height) improved. Conclusion Reduced mean serum zinc levels were observed in children who received standard milk, as well as those who received zinc-fortified milk. These reduction in serum zinc levels may be a part of homeostatic control mechanim for improving the negative zinc balance in zinc pools, as a negative effect on linear growth was not observed. Larger clinical trials of adequate sample size need to be conducted in order to provide better understanding on zinc regulation among underweight school children.