BACKGROUND: Population level data regarding the general mental health status, and the socio-demographic factors associated with the mental health status of adolescents in Australia aged 12-16 years is limited. This study assessed prevalence of mental health problems in a regional population of Australian students in Grades 7-10, and investigated associations between mental health problems and socio-demographic factors. METHODS: A web-based survey was conducted in 21 secondary schools located in disadvantaged local government areas in one regional local health district of NSW Australia. Mental health problems were measured using the youth self-report Strengths and Difficulties Questionnaire (SDQ) total SDQ score and three subscale scores (internalising problems, externalising problems and prosocial behaviour). Associations between each SDQ outcome and student socio-demographic characteristics (age, gender, Aboriginal and/or Torres Strait Islander Status, remoteness of residential location and socio-economic disadvantage) were investigated. RESULTS: Data are reported for 6793 students aged 12-16 years. Nineteen percent of participants scored in the ‘very high’ range for the total SDQ, 18.0 % for internalising problems, 11.3 % for externalising problems and 8.9 % for prosocial behaviour problems. Gender and Aboriginal status were associated with all four SDQ outcomes, while age was associated with two, excluding externalising problems and prosocial behaviour. Aboriginal adolescents scored higher for mental health problems than non-Aboriginal adolescents for all four SDQ outcomes. Females scored higher than males for total SDQ and internalising problems, with mean difference greatest at age 15. Males scored higher for externalising problems and lower for prosocial behaviour than females. CONCLUSIONS: The finding that mental health problems significantly varied by age, gender and Aboriginality may suggest a need for tailored interventions for groups of adolescents with highest levels of mental health problems. Trial Registration ANZCTR ACTRN12611000606987. Registered 14/06/2011.