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Immune system is regulated by circadian rhythms, which promote inflammation and facilitate pathogen elimination. Antimicrobial peptides secreted by milk somatic cells and mammary gland epithelial cells play a crucial role in protecting the mammary gland from pathogenic invasion and mastitis. In this study, we aimed to investigate the circadian rhythms of clock gene and antimicrobial peptide gene expression in goat milk somatic cells, as well as the circadian variation in antimicrobial peptide concentrations in milk. Milk and blood samples were collected from eight goats every 4 h for three days, with light exposure from 6:30 to 19:00. Notably, plasma prolactin level, milk Na+ concentration, and somatic cell count exhibited circadian rhythms (cosinor: P < 0.05; time: P < 0.01). Expression levels of some clock genes (Clock, cryptochrome circadian regulator 2, period circadian regulator 2, and nuclear receptor subfamily 1 group D member 1) exhibited circadian rhythms (cosinor: P < 0.05), whereas those of other clock genes, such as basic helix-loop-helix ARNT-like 1, period circadian regulator 1, cryptochrome circadian regulator 1, and retinoic acid receptor-related orphan receptor-α, did not exhibit circadian rhythms. Among the milk antimicrobial peptides, gene expression level of cathelicidin-7 (cosinor and time: P < 0.05), but not that of lactoferrin (cosinor: P = 0.079), exhibited a circadian rhythm in somatic cells. Additionally, goat β-defensin-1, cathelicidin-7, and lactoferrin levels exhibited circadian rhythms in milk (cosinor and time: P < 0.01). Overall, our results suggest that leukocyte migration and antimicrobial peptide production exhibit circadian rhythms in the mammary glands. These findings provide valuable insights to ensure safe milking conditions by milking during periods of high immune activity in the mammary glands.