Mental health problems including emotional and behavioral problems during puberty may be under influence of different risk factors including cultures, living in urban or rural areas and ethnic factors which may vary between different countries. The main aim of this study is to investigate the profile of emotional and behavioral problems and the role of factors such as age, stage of puberty, ethnicity, rurality and living in urban area, as risk factors in Iranian girls. As a part of a large national study we evaluated the emotional and behavioral problems in different stages of puberty in a community sample of Iranian adolescent girls from public schools that were selected by clustered random sampling method. In all subjects, demographic characteristics, and pubertal stages were measured. Emotional and behavioral problems were evaluated using Strength and Difficulties Questionnaire (SDQ). The associations of age, pubertal development indices, socioeconomic and demographic factors with the behavioral problems were assessed. A total number of 4576 students enrolled the study and responded to the questions. The mean age of participants was 13.83 ± 2.19 years. The mean total score of difficulties in participants was 14.34 ± 5.81. According to these results 813 (17.8%) adolescents had total problem scores higher than Goodman's cutoff points and the most frequent problem domain was conduct problems (20.5%). According to the results the most related variable with the total difficulty score of SDQ were ethnicity, residency in urban areas and development of menstrual cycle respectively. The results of this study showed that the most correlated factors with mental health problems in Iranian girls during puberty are ethnicity, urbanity and development of menstrual cycle.