Nine studies were included in the review. The most consistent finding was a significant alteration of the milk lipidome, characterized by an increase in saturated fatty acids and a depletion of neurocritical lipids, such as glycerophospholipids and nervonic acid. Hypothyroidism was associated with reduced total protein content and downregulation of membrane proteins, including adipophilin and butyrophilin. Additionally, thyroid dysfunction correlated with decreased levels of sialylated oligosaccharides. Conversely, specific immune modulators, such as the Ig gamma-3 chain, were upregulated. This evidence concerns the gene PLIN2 and hypothyroidism.