Abstract: Under nutrition among school-age children have serious consequence on individual and national growth and development. The purpose of this study was to assess the nutritional status of 394 school-age children (7-11 years) attending Conventional Primary Schools (CPS) and Integrated Qur’anic Schools (IQS) in Kaduna. A pretested questionnaire was used to generate information on their socio-economic, food intake pattern and anthropometric status. The mean energy (1861±547.53 23 kcal), protein (32.16±8.93 g), Vitamin A (795.48±183.48 RE), iron (11.61±4.02 mg), iodine (122.65±130.35 mg), calcium (625.38±212.57 g) and Vitamin C (28.09±29.12 mg) intakes were lower for those in CPS compared to their counterparts in IQS facilities. Results showed that about 41.2% of the children were stunted been slightly higher in children attending IQS (9%) than those in CPS but the difference was no significant (p>0.05). Underweight was also generally high (48.7%). There were more (24.6%) cases of overweight among CPS than IQS (22.0%) children and only 1% level of obesity was recorded. Malaria and helminthes infection was not significantly different (p>0.05) among subjects attending CPS and IQS. Correlation between malnutrition and type of school, level of energy intake rate and mother’s educational level showed no relationship (p = 0.05). Data on the prevalence and degree of malnutrition among school-age children attending both CPS and IQS sectors of education in Nigeria is limited.