Purpose Mental health disorders are a pressing issue among adolescents around the world, including in India. A better understanding of the factors related to poor mental health will allow for more effective and targeted interventions for Indian adolescents. Methods The Indian Adolescent Health Questionnaire (IAHQ), a validated questionnaire designed specifically for use in schools, was administered to approximately 1500 secondary students in three private urban Indian schools in 2012. The Strengths and Difficulties Questionnaire (SDQ) module assessed mental health. Linear regression was used to predict SDQ scores. The biopsychosocial framework was used as an organizing framework to understand how each explanatory variable in the final model might impact the SDQ score. Results One thousand four hundred and eight students returned IAHQ surveys (93.9% response rate); 1102 students completed questions for inclusion in the regression model (78.3% inclusion rate). Statistically significant (p < 0.05) independent variables associated with SDQ scores were gender, level of overall health, negative peer pressure, insults from peers, kindness of peers, feeling safe at home, at school, or with friends, and grades. Discussion Schools have a role to play in improving adolescent mental health. Many of the significant variables in our study can be addressed in the school environment through school-wide, long-term programs utilizing teachers and lay counselors. The IAHQ and SDQ can be used by schools to identify factors that contribute to poor mental health among students and then develop targeted programs to support improved mental health.