Although numerous pesticides may interfere with thyroid function, however, epidemiological evidence supporting this relationship is limited, particularly regarding modern non-persistent pesticides. We sought to evaluate the association of agricultural work practices, use of contemporary-use pesticides, and OC pesticides residue levels in serum with circulating thyroid hormone levels in an agricultural population. A cross-sectional study was conducted with a random sample of 275 male and female farm residents in Farroupilha, South of Brazil. Information on sociodemographics, lifestyle and agricultural work was obtained through questionnaire. Blood samples were collected on all participants and analyzed for cholinesterase activity, serum residues of OC pesticides, and levels of free T4 (FT4), total T3 (TT3) and TSH. Non-persistent pesticides exposure assessment was based on questionnaire information on current use of pesticides, and frequency and duration of use, among others. Associations were explored using multivariate linear regression models. Total lifetime years of use of fungicides, herbicides and dithiocarbamates in men was associated with increased TSH accompanied by decrease in FT4, with evidence of a linear trend. In addition, there was an association between being sampled in the high pesticide-use season and increased TSH levels. Conversely, farm work and lifetime use of all pesticides were related with slight decrease in TSH and increased TT3 and FT4, respectively. In general, pesticide use was not associated with thyroid hormones in women. Subjects with detected serum concentrations of β-hexachlorocyclohexane, endrin, dieldrin, heptachlor epoxide B, γ-chlordane, transnonachlor, heptachlor, p,p′-dichlorodiphenylethane and endosulfan II experienced slight changes in TT3; however, associations were weak and inconsistent. These findings suggest that both cumulative and recent occupational exposure to agricultural pesticides may affect the thyroid function causing hypothyroid-like effects, particularly in men.