Intestinal parasites are a major concern in most developing countries. About 60% of the world’s population are infected with intestinal parasites which are commonly associated with HIV/AIDS disease. This study was designed to assess the prevalence of intestinal parasite infections among adult HIV/AIDS patients on ART and those not on ART. This hospital-based prospective study was conducted in three selected HIV Clinics in the Cape Coast Metropolis. A total of 206 HIV positive patients aged from 18 to 65 years, of both sexes, were involved in the study from January 2011 to April 2012. Stool samples were collected from the participants and examined using direct wet mount, formol-ether concentration method, Kato-Katz technique and modified Ziehl-Neelsen (ZN) staining method. Blood samples were taken to analyze their CD4+ T-lymphocyte count at each encounter. The stool examination and blood analysis were repeated on their subsequent visits to the clinic for a period of six months. Questionnaire on sociodemographic and medical history of participants was administered. Data were analysed using SPSS version 19 software and p-value was set at p<0.05.The overall prevalence of intestinal parasites in this study was 47.6 % with a significant difference (p=0.012) between parasite-positive participants on ART (19.9%) and those not on ART (27.7%). Most of the parasite-positive participants (23.3%) had CD4+ counts below 200 cells/µL. Intestinal parasites detected in this study included: Giardia lamblia (18.0%), Entamoeba histolytica (12.1%), Cryptosporidium spp. (5.8%), Isospora belli (4.4%), Strongyloides stercolaris (3.9%), Ascaris lumbricoides (1.9%) and Trichuris trichiura (1.5%). G. lamblia and E. histolytica were the most prevalent. Cryptosporidium spp. (p=0.021) and I. belli (p=0.020) infections were significantly higher in participants who were not on ART, which participants were also significantly associated (p=0.020) with CD4+ counts below 200 cells/µL. G. lamblia (p=0.002), E. histolytica (p=0.028), Cryptosporidium spp. (p=0.021) and I. belli infections (p=0.020) were significantly associated with patients with diarrhoea stools. The overall prevalence of intestinal parasites of the study differed by ART status. Patients on ART had lower prevalence of intestinal parasites and most of the intestinal parasite infections were associated with lower CD4+ counts. This study has established that HIV/AIDS disease coexists with intestinal parasite infections, therefore, stool examination should be reinforced as part of the routine laboratory investigations for the management of HIV/AIDS patients.