Childhood nutritional stunting, an indicator of chronic malnutrition, has been suggested as one factor that can contribute to high incidences of obesity, and impaired lipid and glucose metabolism in developing countries. This study aimed to determine health risks of developing hyperlipidemia, obesity, and diabetes as non-communicable diseases (NCDs) among nutritionally stunted Egyptian children. A total of 90 children were enrolled; 60 nutritional stunted children and 30 non- stunted of matched age and sex. Clinical, demographic characteristics were determined for the studied children. Lipid profile levels, fasting plasma levels of glucose, and insulin were measured in these subjects. Pancreatic beta cells' function (HOMA-β) and insulin resistance (HOMA-IR) were calculated by homeostasis model assessment (HOMA). Stunted children exhibited significantly lower values for weight, weight-for-age Z score (WAZ), height, and height-for-age Z score (HAZ) as compared to normal ones. Significant elevation in total cholesterol (TC), and low density lipoprotein cholesterol (LDL-c), significant decrease in high density lipoprotein cholesterol (HDL-c) and HDL/LDL ratio were detected compared to that of the healthy control subjects. There were no significant differences in the levels of fasting glucose, fasting insulin, homeostasis model assessment of beta-cell function (HOMA-β), and homeostasis model assessment of insulin resistance (HOMA-IR) between the two compared groups. Conclusion: Alterations in lipid pattern among nutritionally stunted Egyptian children may predict the future of NCDs later in life.