Background: This study was designed to describe different oral mucosal changes present in HIV/AIDS patients taking antiretroviral therapy (ART) in Pakistan and to compare these changes with CD4+ lymphocyte count and plasma viral load. Methods: Oral smears, from n=35 patients taking antiretroviral therapy, were prepared and examined microscopically using routine and special stains. CD4+ lymphocyte count was determined using flow cytometry. Latest plasma viral load levels were recorded from the patient`s updated laboratory record and patients were clinically examined and staged according to WHO clinical staging system. Results: Oral lesions were present in 63% of the patients with oral pigmentation in 45.7%, chronic periodontitis in 20%, linear gingival erythema in 2.9%, pseudomembranous candidiasis, oral ulcers and xerostomia each in 5.7% cases while mucositis, oral hairy leukoplakia and oral wart each in 2.9% cases. On cytological examination, fungi were detected in 48.5% smears. Inflammation was seen in 65.7% smears, micronuclei in 51.4%, nuclear atypia in 37.1% and dysplastic changes in 17.1% (grade 1 in 83.3% and grade 2 in 17%) smears. Most of the oral mucosal changes were seen with low CD4+ lymphocyte count but no association was seen with high viral load. Conclusions: This study describes different oral mucosal changes present in HIV/AIDS patients taking antiretroviral therapy (ART) in Pakistan and highlights their importance as a marker of immunosuppression and disease progression as these changes have strong association with low CD4+ lymphocyte count.