Objective To study the impact of wholesome mid day meal (MDM) program run by an NGO on the growth of the primary school students in rural area of Mathura district. Methods This intervention study involved children enrolled in Government run rural primary schools in Mathura district in Uttar Pradesh from March 06 through August 07. A wholesome, nutritionally balanced MDM provided by an NGO for the students in the 6 primary schools was selected as intervention group. Control group consisted of children in 8 schools which received locally prepared MDM by village panchayats. Height, weight, change in height/month, change in weight/month, prevalence of protein-energy malnutrition and prevalence of signs of vitamin deficiencies, were measured. Results Food was provided for 221 days in one year. Within group and between groups repetitive measures were compared using generalized estimating equation (GEE). Within both intervention and control groups height and weight had significantly increased (p < 0.05), while there was no significant difference between the groups. There was no change in prevalence of malnutrition within either of the groups. Reduction in vitamin A deficiency signs was 38% more in intervention group (p < 0.001). Prevalence of Vitamin D deficiency reduced by 50% more in intervention group. No such differences between groups were observed for vitamin B complex and vitamin C. Conclusions MDM provided by the NGO has no better impact on growth of the primary school children, however, it reduced prevalence of vitamin deficiency significantly in comparison to the MDM run by Village Panchayats.