In this study, we investigated the fat depot-specific expression of immune cell marker genes of regulatory T-cells (FOXP3), T lymphocytes (CD3E), B lymphocytes (CD79A), and macrophages (CD68) in fattening Wagyu cattle at three anatomical sites (subcutaneous, intramuscular, and visceral adipose tissue). The expression of the FOXP3 gene in subcutaneous adipose tissue was significantly higher than in intramuscular and visceral adipose tissue. In contrast, the expression of CD3E, CD79A, and CD68 genes in visceral adipose tissue was significantly higher than in subcutaneous and intramuscular adipose tissue. These results indicate that the anatomical location of bovine adipose tissue influences immune cell populations in a fat depot-specific manner.