Data concerning any difference in serum lipid profiles and glucose level after patients switched from stavudine to zidovudine in Ethiopia is very limited. Seventy eight adults receiving antiretroviral therapy (ART) that included stavudine/lamivudine with either of efavirenz or nevirapine during ART initiation were enrolled. Of these patients, 53 were switched to zidovudine/lamivudine/nevirapine (NVP-group) and the rest 25 were switched to zidovudine/lamivudine/efavirenz (EFV-group). Serum lipid profiles and glucose were determined after overnight fasting. Dyslipidemia and dysglycaemia were assessed according to the United State National Cholesterol Education program-III guideline. Statistical analysis was done using Statistical Package for Social Sciences (SPSS) Version 20. Of the 78 patients, 39.7% were males and 60.3% were females. At the end of the study follow-up, the prevalence of TC ≥ 200 mg/dl, LDL-c ≥ 130 mg/dl, TG ≥ 150 mg/dl, HDL-c < 40 mg/dl and glucose ≥ 110 mg/dl were higher in EFV group when compared with NVP. About 74.4% patients had at least two laboratory abnormities which is compatible with a diagnosis of dyslipidemia at 12 month of post switch. Four lipid profiles abnormal within a single individual was 16% in EFV and 3.8% in NVP group, p = 0.08. Raised HDL-c concentration was observed in NVP group in both periods when compared with EFV. In addition, patients that switched from d4T/3TC/NVP to AZT/3TC/NVP had a significant change in TC and TG (p = 0.001 for both). Also TC ≥ 200 mg/dl was decreased from 49 to 16% (p = 0.04). Furthermore, sex was significantly and negatively associated with raised TC and TGs among patients using NVP based regimen. Raised HDL-c concentration, decreased proportion of abnormal lipid profiles and abnormal glucose was observed in the NVP group. Based on these findings, NVP may be expected to reduce the risk of cardiovascular diseases.