Background In collaboration with two health facilities and a mobile clinic, Counselling and Testing (CT) services was implemented in two departments of Benin (Atacora and Donga) trough a project funded by the Kreditanstalt für Wiederaufbau (KfW) Germany. These interventions targeted vulnerable youth (15–24) and included STI prevention, screening and management, using clinical screening algorithms. 28 868 clients requesting HIV counselling and testing were registered from 2007 to 2009 trough a database.

Objectives To assess rate and risks factors of STI among vulnerable youth attending counselling and testing facilities, including STI management.

Methods Descriptive analysis and logistic regression was performed on the database with SPSS 17. The dependent variable is “having had an STI the last 3 months”. The independents variables are—“having multiple partners in the three past months”, “consistent use of condom” and socio-demographic characteristics.

Results In all 5.1% of HIV counselled and tested clients approached for STI on-site screening had STI the last 3 month, while STI prevalence among this population is 1.9%. Multiple partners (OR=4.5; p=0.000), no consistent use of condom (0R=1.3; p=0.002) were significantly associate to IST infection. The level of instruction (OR=1.3; p=0.000) and sex (OR=0.6; p=0.000) were the significant socio-demographic characteristic associated with STI.

Conclusions Data findings indicate that having had STI in the last 3 month may be a motivation for youth which are attending HIV counselling and testing facilities in Atacora/Donga in Benin, and “high numbers of partners” is the main risk factor for STI among them. Then, scaling up HIV counselling and testing services may be a right way for STI prevention, screening and management. Finding suggests that such intervention (counselling) focused on reducing number of partner, improved to promotion of condom use, may reduce STI incidence among vulnerable youth that need further investigation.