Adolescence is a nutritionally vulnerable time when rapid physical growth increases nutrient demand. Addressing the nutrition needs of adolescents could be an important step toward breaking the vicious cycle of intergenerational malnutrition. Under the healthy school initiative, a baseline assessment was carried out to assess the nutritional status, dietary habits, and personal hygiene of school-going adolescents to plan the future interventions at school level. A cross-sectional study was conducted in two government-aided schools for 6 months among 814 students of Class VI-IX to assess their dietary habits and personal hygiene by using the GSHS( Global School based student Health Survey) -2007(Indian version) tool. Anthropometric measurement was taken by standard technique. The study found the proportion of thinness, stunting, and overweight/obesity as 40%, 20%, and 4.2%, respectively. Male students were found more thin (61.1% vs. 38.8%) and stunted (55.6% vs. 44.4%) as compared to female students. Less than one-fourth (13.7%) of the students reported <5 servings of fruits and vegetables. In multivariable analysis, male students, children of homemaker mother, skipping breakfast on all days of week, consumption of fast food ≥3 times/week, consumption of high sugary ready to use food, and infrequent handwashing after toilet were found to be predictors of thinness. Dietary habits and personnel hygiene were found to be important factors of undernutrition; promoting health behavior through school health policy with involvement of teachers, students, and parents is highly recommended to reduce the problem of undernutrition among adolescents.