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Background: Health status of children and adolescents is determined to a larger extent by their nutritional status. There are no published studies available on the influence of thinness on childhood morbidity using new World Health Organization-body mass index (WHO-BMI) for age criteria. Methods: This cross-sectional study was conducted in primary, high schools, pre-university and degree colleges at southern Karnataka for a period of 1 year. Results: Majority 6924 (53.6%) were in the age group of 15-19 years with the mean age of 14.2 ± 3.1 years. 6167 (47.7%) were males and 6749 (52.3%) were females. As per WHO growth standards for children between 5 and 19 years, taking BMI for age criteria into account, 9092 (70.4%) subjects were found to be normal, 3660 (28.3%) thin and 164 (1.3%) overweight/obesity. 8224 (63.7%) subjects were suffering from some sort of morbidities. Mean morbidities rank for subjects with thinness was found to be significantly higher compared with normal and overweight/obese subjects. Thinness was found to be the major predictor of morbidity age, sex and residing in rural areas. Conclusions: Magnitude of thinness among children and adolescents was 28.3%. BMI for age criteria was found to be a significant predictor of childhood and adolescent morbidity.