The objective of this study was to evaluate the frequency of thyroid function alterations and its associated factors in a group of patients from a university hospital in Colombia.From June 2007 through June 2008, 636 HIV patients were followed in order to assess the relation of thyroid function with the use of HAART.The overall prevalence of hypothyroidism (TSH > 4.6 μUI/mL) was 15.5% (100/636). The association of hypothyroidism in the independent analysis showed significant relation only for the use of nevirapine (RR 1.6; CI 95% 1.1- 2.34) and stavudine (RR 1.5; CI 95%, 1 - 2.3).The prevalence of hypothyroidism was surprisingly high among the studied population.