OBJECTIVES: To document risk behaviours and prevalence of chlamydia and gonorrhoea infections among adolescents aged 14 to 17 years entering care in Quebec Youth Protection Centres (YPC). METHODS: From July 2008 to May 2009, adolescents residing in six YPCs completed a questionnaire during a face-to-face interview. Questions covered sexual and substance use behaviours prior to admission, as well as other health issues affecting respondents' mental and physical health. Urine samples were tested for Chlamydia trachomatis genital infection (CTGI) and Neisseria gonorrhoea genital infection (NGGI). RESULTS: Among 578 participants aged 14 to 17 years, 89% had had consensual sexual relations. Sexual risk behaviours included early sexual initiation (66% at <14 years); multiple partners (median lifetime number: girls 5, boys 8); 50% or more of sexual relations under the influence of drugs or alcohol (girls 43%, boys 48%); group sex (girls 38%, boys 43%); and sex in exchange for money or other goods (girls 27%, boys 8%). Only a quarter of boys and girls used double protection (condom and a contraceptive method) during the most recent vaginal relation. A history of pregnancy was reported by 28% of girls. Prevalence of CTGI was 9.3% (CI: 5.5-14.5) among girls and 1.9% (CI: 0.6-4.4) among boys. Prevalence of NGGI gonorrhoea was 1.7% (CI: 0.3-4.8) among girls and 0% (CI: 0.0-1.4) among boys.In multivariate analyses, factors significantly associated with chlamydia infection among sexually active girls were: hospitalization for alcohol intoxication; and a history of suicidal ideation with plan. CONCLUSION: Sexual risk behaviours are common among adolescents entering YPCs, resulting in high levels of chlamydia infection. Mental health issues such as substance misuse and serious depressive symptoms are associated with these high rates. A youth's stay in these facilities is an opportune time to screen not only for sexual risk behaviours but also for mental health problems; appropriate risk reduction education and referrals can then be provided as needed.