Biodiesel or renewable diesel fuels are alternative fuels produced from vegetable oil and animal tallow that are being considered to help reduce the use of petroleum-based fuels and emissions of air pollutants including greenhouse gases. Here, we analyzed the gene expression of inflammatory marker responses and the cytochrome P450 1A1 (CYP1A1) enzyme after exposure to diesel and biodiesel emission samples generated from an in-use heavy-duty diesel vehicle. Particulate emission samples from petroleum-based California Air Resource Board (CARB)-certified ultralow sulfur diesel (CARB ULSD), biodiesel, and renewable hydro-treated diesel all induced inflammatory markers such as cyclooxygenase-2 (COX)-2 and interleukin (IL)-8 in human U937-derived macrophages and the expression of the xenobiotic metabolizing enzyme CYP1A1. Furthermore, the results indicate that the particle emissions from CARB ULSD and the alternative diesel fuel blends activate the aryl hydrocarbon receptor (AhR) and induce CYP1A1 in a dose- and AhR-dependent manner which was supported by the AhR luciferase reporter assay and gel shift analysis. Based on a per mile emissions with the model year 2000 heavy duty vehicle tested, the effects of the alternative diesel fuel blends emissions on the expression on inflammatory markers like IL-8 and COX-2 tend to be lower than emission samples derived from CARB ULSD fuel. The results will help to assess the potential benefits and toxicity from biofuel use as alternative fuels in modern technology diesel engines.