Background: Zinc and iron belong to the group of 10 essential micronutrients; their deficiency may be an important cause of idiopathic short stature.Objectives: The aim of this study is to assess serum level of micronutrients zinc and iron and the nutritional status in a group of prepubertal children with idiopathic short stature and to compare these data with normally growing children.Patients and methods: The present work is a cross-sectional study was done in National Nutritional Institute (NNI). It included 40 pre pubertal children with a mean age 7.9 years ± 1.05 SD, complaining of idiopathic short stature, with mean height SDS -2.42 ± 0.59 SD, sex and age matched to 40normally growing children.Anthropometric measurements (height, weight) were assisted. Analysis of serum iron, zinc and Hb. Dietary assessment was done by 24hrs recall for 3 days, all data statistically analyzed by SPSS program. Results: Significant difference in serum zinc (p =0.00) between the 2 groups but there was no significant difference in serum iron (p = 0.68). Prevalence of zinc deficiency was (58.7%) in our study group. Dietary assessment showed significant difference in total energy and zinc (p = 0.01and 0.00 respectively). Conclusions: zinc and iron deficiency may be the cause of idiopathic short stature, so, serum measurement and dietary assessment of zinc and iron is important for the case.