Background: Highly active antiretroviral therapy (HAART) has transformed HIV into a manageable chronic condition but is associated with dyslipidemia, increasing cardiovascular disease (CVD) risk. Data on lipid profile alterations in rural South Africa primary healthcare settings remain limited despite high HIV burdens. The purpose of the study was to determine the prevalence of lipid profile alterations among adult HIV patients receiving HAART at rural Eastern Cape primary healthcare facilities. Methods: Retrospective cross-sectional analysis of clinical and laboratory records from 370 adults (>18 years) on HAART at five OR Tambo District health care facilities (2020 – 2024) Lipid parameters (Total cholesterol {TC} LDL Cholesterol< HDL cholesterol, Tri-glycerides {TG} from National Health Laboratory Services (NHLS) data base were assessed NCRP ATP III thresholds. Prevalence was calculated with SPSS v29.0; overall dyslipidemia defines as any abnormality. Results: High prevalence of lipid alterations was observed: hypercholesterolemia 53.8 % (199/370). Overall dyslipidemia affected 80.8 % (299/370) of patients, confirming substantial metabolic burden in this rural cohort. Conclusion: Over 80% of rural HAART patients exhibited dyslipidemia predominantly elevated LDL-cholesterol, LDL+C (61.4%) and triglycerides (60.5%) Findings underscore urgent need for routine lipid screening, regimen optimization toward integrase strand transfer inhibitors. (INSTIs) and NCD-HIV integration in South Africa’s primary healthcare system to mitigate CVD risk.