Introduction: Micronutrient deficiencies are prevalent in infancy and childhood where there is rapid growth and a concomitant high nutritional demand, particularly in developing countries. Other vulnerable periods are adolescence and pregnancy. Among micronutrients, iron is the most common nutritional deficiency in the world and is the major cause of anemia. Aim of work: The aim of this work was to study iron and zinc status among 12-16 years children with short stature for age. Materials and Methods: A case-control study was conducted including forty12-16 years children (20 cases and 20 controls). Cases were children with short stature for age, attending the outpatient clinic of endocrinology department at Ain Shams University Hospitals (20 children). Controls were matched group selected from normal height-for-age children attending the outpatient clinic for another cause according to the inclusion criteria. All children were subjected to full laboratory assessment of serum iron and zinc in addition to complete blood picture and stool analysis. Socio-demographic, family and developmental histories were taken in addition to physical examination including height, weight, and secondary sexual characteristics. Results: The mean serum iron, serum ferritin and serum zinc level were significantly lower among cases than controls (61.5±3.65, 24.5±2.36 and 54.3±5.65 versus 66.8±4.32, 32.5±5.32 and 70.6±6.22 respectively). Regarding Total Iron Binding Capacity (TIBC); the mean values were 325.6±109.58 among cases compared to 198.6±56.8 among controls with statistically significant difference between them (p<0.05). There were significant positive correlations between serum iron level, serum ferritin and serum zinc level versus hemoglobin concentration and WBCs count. However, there was a significant negative correlation between iron binding capacity of stunted children and their hemoglobin concentration and WBCs count. There was no statistically significant correlations between them and weight or height of stunted children. Males had higher hemoglobin concentration, RBCs count and serum iron level compared to females (11.5±1.4, 3.8±0.9 and 65±3 compared to 
10±1.2, 3.2±0.7, 60.5±4 respectively). Conclusion: Serum iron and serum zinc levels significantly decreased in children with short stature compared to normal children and their levels had positive linear correlation with hemoglobin concentration and WBCs count.