Introduction: The life of an adolescent in a school hostel is well-managed with respect to daily food intake and physical activity. These adolescents are likely to be physically active and are assumed to consume nutritious food. However, little is known about malnutrition and factors related to it. Thus, this study determined the association between malnutrition (thinness & overweight) and socio-demographic characteristics of these adolescents living in day-school hostels. Methods: Data from Program Cara Hidup Sihat (Healthy Lifestyle Program), comprising a total of 4189 13-year-old school-going adolescents were used. A multi-stage stratified cluster sampling method was applied. Information on socio-demographic characteristics was collected using self-administered questionnaires. Body weights and heights were measured. Body mass index (BMI)-for-age (z-score), or BAZ, was determined using the World Health Organization's (WHO) Growth Reference. Results: The prevalence of overweight (23.3%, 95% CI: 22.1, 24.7) was about six times higher than thinness (4.3%, 95% CI: 3.7, 5.0). Males had higher prevalence of thinness (5.6%, 95% CI: 4.6, 6.9) compared to females (3.4%, 95% CI: 3.7, 4.2). A higher prevalence of overweight was observed in the central zone than in the other five zones. Complex samples logistic regression showed that adolescents from the central zone and those with monthly parental incomes a RM 5000 were 2.5 times (adjusted odds ratio [OR]=2.5, 95% confidence interval [CI]: 1.6, 3.9) and 2.0 times (adjusted OR=2.0, 95% CI: 1.3, 2.9), respectively, more likely to be at risk of overweight compared to adolescents from the other five zones and with parents whose monthly incomes were less than RM 5000. Conversely, male adolescents were 1.7 times more likely to be at risk of thinness (adjusted OR=1.7, 95% CI: 1.2, 2.3) compared to female adolescents. Conclusion: The dual forms of malnutrition co-existed, with over-nutrition being more prevalent than under-nutrition. Future healthy body weight intervention programs should consider sex, monthly parental incomes and geographic zones of adolescents living in day-school hostels.