Background: Rapidly changing physical environment has led to socio-demographic mutilation among populations, increasing the prevalence of dual burden of malnutrition especially among school going children. Objective: The study aimed to assess the effect of dietary habits and parental history of chronic disease on prevalence of dual burden of malnutrition among school children. Design: Multistage cluster sampling technique was applied to select 10/113 public-private schools. Students of 4th to 9th standard (n= 6472) were enrolled under the study. Standard techniques were used to derive the anthropometric measurements. Information on the dietary habits and parental history of chronic degenerative diseases was elicited using structured questionnaire. Results: Eating habits were categorized under high, moderate and low risk based on the frequencies. Frequency of eating out of home was at moderate risk among 15% students. Moderately risky eating behavior prevailed among 13% - 21% students. Consumption of maggie noodles was maximum (21%), followed by ice-cream (18%), chips (17%) and soft drink (11%). Moreover consumption of junk food, fried food and sweets have shown a significant co-relation with the nutritional status of children at p value <0.05, 95% CI. Both father and mother of 8.2% children have reported to be suffering from either of the chronic diseases such as obesity, diabetes, hypertension, stroke and heart disease. Parental history of obesity followed by heart disease significantly correlated with the current nutritional status of the children. Conclusion: Unhealthy eating habits and parental history of diseases determine the shift in nutritional status of children from a young age.