This study was conducted on 193 children aged 6-12 years. They were 93 children (65 boys and 28 girls) living in two residential institutions in Cairo and 100 non-instituted children (65 boys and 35 girls) who are their matched school peers. Anthropometric measurements, complete physical examination and laboratory investigations including haemoglobin concentration, complete urine and stool analysis were performed to all children. Results showed that 25.81% of instituted children have body weights below the 10th percentile and 60.22% have heights below the 10th percentile compared to 14% and 37% of non-instituted children respectively. The differences were statistically significant. The prevalence of vitamin deficiency manifestations, and skin diseases was significantly higher in the instituted group. The mean haemoglobin concentration was lower in the instituted children, with a significant difference in all males and in females aged 9-12 years. Intestinal parasitic infections were more prevalent in the instituted children. It was found that among instituted children weight and height were most affected by cause of institution and number of children cared for by a substitute mother while hemoglobin concentration was most affected by age at institution and the level of education of the substitute mother.