This research is a cross-sectional study to investigate the association between CD4+ cell count, intestinal parasites and diarrhea in HIV infected patients in Khartoum State, Sudan between the years 2007 – 2010. The study was conducted on 657 HIV infected and non-infected patients, of the study sample 423 were HIV positive patients. The HIV positive patients in the sample were divided into two categories the first on ART and the second without ART. Stool samples were collected from patients to diagnose parasitic infections by examination of a single stool specimen as fresh wet mount preparation, formol-ether concentration technique and staining. CD4 counts were recorded to assess the status of HIV infection vis-à-vis parasitic infection. The results showed that diarrhea was more prevalent in HIV infected than in HIV non-infected patients. Patients with chronic diarrhea had lower CD4 cell counts. The study reached very significant and important conclusions in the association between CD4+ cell count, intestinal parasites and diarrhea which all can lead to better diagnose for the treatment of HIV infected patients.