Background: In developing countries, malnutrition is a major health problem with prevalence ranges of 4-46%. Early childhood malnutrition is irreversible and intergenerational, with adverse consequences on adult health. Objective: This study aimed to determine the current prevalence and some associated risk factors of anemia, anthropometric indices and intestinal parasitic infection among primary school children in Alexandria, Egypt. Methods: A cross sectional study was carried out on 330 school children aged 6-12 years, attending governmental primary schools, in Alexandria. The sample was selected using a multistage random cluster sampling technique. Nutritional status of these children was determined using age and the anthropometric parameters of weight and height. z-scores of height-for-age, weight-for-age and weight-for-height were computed. Epi Info 2000 software was used to evaluate the anthropometric results of each individual. Cyanmethaemoglobin method and two Kato thick smear technique were employed to identify blood hemoglobin and parasites respectively. Data were analyzed using appropriate descriptive, univariate and multivariate logistic regression methods. Results: Underweight, stunting, wasting, anemia and intestinal parasitoses were 4.2%, 3%, 3.7%, 84.5% and 33.6 % respectively. Parasites encountered during the study were Ascaris lumbricoides (24.6%), Trichuiris trichiura (19.6 %), and Enterobius vermicularis (3%) respectively. Based on multiple logistic regression analyses, the main risk factor for stunting was the presence of parasitic infection (OR= 4.85; 95%CI=1.23-19.12). The risk factors for anemia were age ≥10 years (OR= 8.79; 95% CI= 2.01-38.35), and presence of parasitic infection (OR= 2.26; 95% CI= 1.07- 4.82), while the risk factors for parasitic infection were age 8 -10 years (OR = 1.94; 95% CI = 1.13 - 3.34; p= 0.02),and age ≥10 years (OR= 1.99; 95% CI= 1.05-3.79; p= 0.035), anemia (OR= 2.1; 95% CI = 0.99-4.44; p= 0.054) and stunting (OR= 4.33; 95% CI= 1.05-17.83; p= 0.042). Conclusion: Findings from this study are strongly suggestive that intestinal parasitic infections and malnutrition exist in school children residing in Alexandria and constitute a major health problem that needs to be addressed immediately to reduce morbidity and mortality.