Objective To investigate the expression level of free fatty acid receptor 4 (FFAR4) and its correlation with cytokine expressions in peritoneal macrophages and alveolar macrophages. Methods Peritoneal macrophages and alveolar macrophages were purified and collected using flow cytometry from adult BALB/c mice. Real-time quantitative PCR was used to measure mRNA expression levels. The correlation between FFAR4 expression level and cytokine expression levels was analyzed using linear regression. Results The expression levels of FFAR4, interleukin-1 (IL-1) and tumor necrosis factor-alpha (TNF-α) were significantly higher in the alveolar macrophages than in the peritoneal macrophages. In contrast, the expression levels of IL-10 and IL-6 were significantly lower in the alveolar macrophages than in the peritoneal macrophages. In the peritoneal macrophages, FFAR4 expression was positively correlated to the mRNA expressions of IL-10, IL-6 and TNF-α, but negatively correlated to IL-1 mRNA expression. In the alveolar macrophages, FFAR4 expression was positively correlated to the mRNA expressions of IL-1, IL-6 and TNF-α, but negatively correlated to IL-10 mRNA expression. Conclusion FFAR4 is differentially expressed and correlated to cytokine expressions in peritoneal macrophages and alveolar macrophages from BALB/c mice.