There is a paucity of information about the factors associated with oral colonization with Candida species and the changes associated with antiretroviral (ARV) therapy. This study investigated the role of ARV therapy and other factors in a study population. Relevant clinical and laboratory information was obtained and oral rinse specimens were tested for yeast identification. The findings were compared with previous data from the same clinic before ARV therapy was available. Of 197 patients, 117 (59.4 %) were colonized. Candida albicans was the dominant species (71 %) and Candida dubliniensis was the most frequent non-albicans Candida. The colonized group had a higher rate of concurrent tuberculosis (TB) infection (77.4 % compared with 56 % in the non-colonized patients, P50.03) and a lower median CD4+ count (346.5 cells . Participants not on ARV therapy and those having oral prosthesis were all colonized (P50.003 and P50.022, respectively). The oral Candida count was negatively correlated with the CD4 + count in participants on ARV therapy (P50.006). Associated factors using logistic regression were dental caries (odds ratio51.30; 95 % confidence interval51.07-1.60] and diabetes mellitus (odds ratio55.52; 95 % confidence interval51.68-18.12). The colonization rate was higher (81.3 %) as well as the yeast count before ARV therapy was available, while the prevalence of C. dubliniensis was found to have increased from 6.3 to 11 %. Dental caries, diabetes mellitus, oral prostheses and TB infection were associated with oral colonization. The colonization rate, variety and yeast counts declined with ARV therapy.