Introduction: Good data on the epidemiology of modes of transmission of HIV among population at risk are important for development of prevention strategies, and resource allocation for the implementation of the interventions. We sought to estimate new HIV infections among key risk groups in Togo. Methods: We conducted a systematic review of epidemiological data on HIV and AIDS as part of the HIV control strategies in Togo from 2001 to 2012 following the PRISMA guidelines. We used the Mode of Transmission (MoT) modelling tool to estimate the incidence of new HIV infections in high risk groups. The MoT tool was developed and validated by UNAIDS and implemented by several countries using data on the HIV epidemic to estimate new HIV infections that will appear in the core groups. We used Epi-MoT tool to assess the availability and the quality of data. A score of availability of data over 50% and the quality over 1.5 were required to proceed to the MoT analysis. Uncertainty analysis to assess the reliability of the results was performed. Results: Incidence of new HIV infections was estimated at 6,643 (95% CI = 5274, 9005) with an incidence rate of 203 per 1,000,000 inhabitants. The proportion of new HIV infections was 61.9% (95% CI = 46.2 to 71.7) in stable heterosexual couples compare to 14.01% (95% CI = 7.2 to 23.3) in people having casual sex. In high-risk groups new HIV infections accounted for 2.4% among sex workers (SWs) (95% CI = 1.2 - 4.1), 7.9% among clients of SWs (95% CI = 3.9-14.1) and 6.9% among men who have sex with men (MSM) (95% CI = 3.1 to 13.1). Conclusion: We describe the prediction of the HIV epidemic with a large contribution of stable heterosexual couples in the occurrence of new infections. But HIV incidence remains high in key risk populations. Innovative strategies for risk reduction should be strengthened to reduce the transmission especially in stable heterosexual couples.