Hypothyroidism is a common thyroid dysfunction with a higher prevalence in women. Impairments in the regulation of basal metabolism, small intestine nutrient transporter, dyslipidemia, and disruption in circadian clocks have been associated with the thyroid disorder. This study aimed to evaluate whether hypothyroidism affects the small intestine circadian clock and the daily expression pattern of gut nutrient transporters in female mice. Adult female C57BL/6J mice were subjected to hypothyroidism by the administration of methimazole (0.1%) and sodium perchlorate (1%) in drinking water for 45 days. After, the animals were subdivided and euthanized every 4 h over the 24 h period under deep anesthesia. The proximal small intestine segment was collected and immediately frozen for gene expression analysis of circadian core clock components (