HIV-1 genotypic diversity in southern Ghana is extensive but other parts are currently under investigated. The study was conducted mostly in the mid and northern sections of Ghana to explore the genetic diversity and phenotypic characteristics of HIV-1 strains in such regions of Ghana. Also ahead of antiretroviral therapy (ART), the study investigated the RT domain of the pol gene for evidence of drug resistance mutations in this naive population. Implications of this observation for therapy in Ghana were explored in the run-up to the initiation and upscaling of ART.