Occupational and environmental exposure to pesticides has been associated with thyroid dysfunction, particularly changes in circulating thyroid hormone levels (T3, T4) and thyroid stimulating hormone (TSH). This study assessed the association between environmental exposure to pesticides and the risk of developing thyroid diseases. A population-based case-control study was carried out among Spanish populations living in areas categorized as of high or low pesticide use according to agronomic criteria, which were used as surrogates for environmental exposure to pesticides. The study population consisted of 79.431 individuals diagnosed with goiter, thyrotoxicosis, hypothyroidism, and thyroiditis (according to the International Classification of Diseases, Ninth Revision) and 1.484.257 controls matched for age, sex and area of residence. Data were collected from computerized hospital records for the period 1998 to 2015. Prevalence rates and risk of having thyroid diseases were significantly higher in areas with higher pesticide use, with a 49% greater risk for hypothyroidism, 45% for thyrotoxicosis, 20% for thyroiditis and 5% for goiter. Overall, this study indicates an association between increased environmental exposure to pesticides as a result of a greater agricultural use and diseases of the thyroid gland, thus supporting and extending previous evidence. This study also provides support to the methodology proposed for real-life risk simulation, thus contributing to a better understanding of the real life threat posed by exposure to multiple pesticides from different sources.