OBJECTIVES: Highly active antiretroviral therapy (HAART) was available for HIV-infected patients in Taiwan since 1997. HAART can effectively reduce mortality and morbidity, but it may also increase the risk and related drug costs of metabolic co-morbidities for HIV-infected patients. The aim of this research was to investigate the prevalence and treatment costs of metabolic co-morbidities such as diabetes, hypertension, and hyperlipidemia between HAART treated and not treated patients. METHODS: We conducted a population-based study using 1M sampling version of the National Health Insurance Research Database (NHIRD) from Taiwan between 2010 and 2012. We extracted HIV-infected patients from both outpatient and inpatient with primary or secondary diagnosis of HIV (ICD codes 042-044). Treatments such as HAART and other related information were extracted. The prevalence and related drug costs of metabolic co-morbidities was estimated and comparison were made using SAS version 9.3. RESULTS: In the sampling database, there were 488 and 235 HIV-infected patients with and without HAART treatments. They were mainly male (94.6% vs. 90.2%, p = 0.0255), HAART treated patients were older than those without (37.5 vs. 34.5, p = 0.0017). The prevalence rate among all patients were 7.6% for diabetes, 13.3% for hypertension, 23.4% for hyperlipidemia, as compared to 3.4%, 8.5% and 6.8% in patients without HAART. There were statistically significant differences for diabetes (p = 0.0294) and hyperlipidemia (p < 0.0001). The difference for hypertension is boradline statistically significant (p = 0.0601). The mean expenditure per patient per year of dyslipidemia drugs, hypoglycemic drug, antihypertensive drug, and sedative hypnotic drug were not statistically significant.  CONCLUSIONS: Per previous literature reviews, the prevalence of diabetes, hypertension, hyperlipidemia for HIV-infected patients with HAART was confirmed and increasing year by year using the real world data in Taiwan. Good control of metabolic co-morbidities to reduce the risk of morbidity and mortality is highly recommended.