Background: The highly active antiretroviral therapy (HAART) has altered the course of HIV infection, transforming it from a fatal illness to a chronic condition, reducing morbidity and mortality. However, this therapy has led to an increased incidence of metabolic problems such as insulin resistance, dyslipidemia, lipodystrophy and impaired glucose metabolism. The objectives of this study are to determine the prevalence of insulin resistance (IR) in a cohort of human immunodeficiency virus (HIV)-infected patients on highly active antiretroviral therapy (HAART) and to investigate the potentially associated factors. Methods: We conducted a cross-sectional study including 219 adult patients with HIV on HAART. IR was determined through the homeostasis model assessment (HOMA-IR) mathematical model, using fasting plasma glucose (FPG) and insulin. Bivariate and multivariate analyses were performed to assess the association between demographic information, clinical characteristics and laboratory results, and IR. Results: 75 (34.2 %) [95 % confidence interval (CI) 28.9-40.9] HIV-patients on HAART showed IR. 61 (81 %) of these patients were on HAART for more than one year, which was mainly composed by non-protease inhibitors drugs (88 %). Metabolic syndrome (MS) was found in 59 (26.9 %) subjects. In the multivariate analysis, the factors associated with IR were age ≥46 years (Prevalence ratio = 2.767, 95 % CI 1.325 to 5.780) and greater body mass index (BMI) (Prevalence ratio = 1.148, 95 % CI 1.054 to 1.250). Conclusions: The prevalence of IR was 34.2 %. Factors associated with IR were age and BMI. We did not find any significant association between IR and protease inhibitors (PI), which may be explained by the small number of patients using PI as part of their HAART regimen included in our study.