Objective To estimate the prevalence of multimorbidity and complex multimorbidity in rural workers and their association with sociodemographic characteristics, occupational contact with pesticides, lifestyle and clinical condition. Methods This is a cross-sectional epidemiological study with 806 farmers from the main agricultural municipality of the state of Espírito Santo/Brazil, conducted from December 2016 to April 2017. Multimorbidity was defined as the presence of two or more chronic diseases in the same individual, while complex multimorbidity was classified as the occurrence of three or more chronic conditions affecting three or more body systems. Socio-demographic data, occupational contact with pesticides, lifestyle data and clinical condition data were collected through a structured questionnaire. Binary logistic regression was conducted to identify risk factors for multimorbidity. Results The prevalence of multimorbidity among farmers was 41.5% (n = 328), and complex multimorbidity was 16.7% (n = 132). More than 77% of farmers had at least one chronic illness. Hypertension, dyslipidemia and depression were the most prevalent morbidities. Being 40 years or older (OR 3.33, 95% CI 2.06-5.39), previous medical diagnosis of pesticide poisoning (OR 1.89, 95% CI 1.03-3.44), high waist circumference (OR 2.82, CI 95% 1.98-4.02) and worse health self-assessment (OR 2.10, 95% CI 1.52-2.91) significantly increased the chances of multimorbidity. The same associations were found for the diagnosis of complex multimorbidity.