Over the past decade, soy biodiesel (BD) has become a first alternative energy source that is economically viable and meets requirements of the Clean Air Act. Due to lower mass emissions and reduced hazardous compounds compared to diesel combustion emissions (CE), BD exposure is proposed to produce fewer adverse health effects. However, considering the broad use of BD and its blends in different industries, this assertion needs to be supported and validated by mechanistic and toxicological data. Here, adverse effects were compared in lungs and liver of BALB/cJ mice after inhalation exposure (0, 50, 150, or 500 μg/m 3 ; 4 h/d, 5 d/wk, for 4 wk) to CE from 100% biodiesel (B100) and diesel (D100). Compared to D100, B100 CE produced a significant accumulation of oxidatively modified proteins (carbonyls), an increase in 4-hydroxynonenal (4-HNE), a reduction of protein thiols, a depletion of antioxidant gluthatione (GSH), a dose-related rise in the levels of biomarkers of tissue damage (lactate dehydrogenase, LDH) in lungs, and inflammation (myeloperoxidase, MPO) in both lungs and liver. Significant differences in the levels of inflammatory cytokines interleukin (IL)-6, IL-10, IL-12p70, monocyte chemoattractant protein (MCP)-1, interferon (IFN) γ, and tumor necrosis factor (TNF)-α were detected in lungs and liver upon B100 and D100 CE exposures. Overall, the tissue damage, oxidative stress, inflammation, and cytokine response were more pronounced in mice exposed to Address correspondence to Dr. Anna A. Shvedova, Pathology and Physiology Research Branch (MS-2015), 1095 Willowdale Road, Morgantown, WV 26505, USA. ats1@cdc.gov. This article is not subject to U.S. copyright. Epidemiologic and occupational studies demonstrated that ambient particular matter (PM) and diesel exhaust particles exert deleterious effects on human health, including exacerbation of preexisting lung disease, increased incidence of respiratory infections, decrement in lung capacity, and enhanced risk of lung cancer (Sawyer et al., 2010;LaGier et al., 2013). According to the U.S. Environmental Protection Agency (EPA), elevated levels of airborne PM, nitrogen oxides, and sulfur oxides contribute to serious health problems in the United States, producing increased acute respiratory symptoms, chronic bronchitis, and aggravation of asthma, cardiovascular diseases, and premature mortality (Ghio et al., 2012). The International Agency for Research on Cancer (IARC) recently identified diesel combustion emissions (CE) as a Group 1 human carcinogen after chronic exposure (Benbrahim-Tallaa et al., 2012). Diesel exhaust particles are mainly aggregates of spherical carbon particles coated with inorganic and organic substances. The inorganic fraction primarily consists of small solid carbon (or elemental carbon) PM ranging from 0.01 to 0.08 microns in diameter. The organic fraction is composed of organic compounds such as aldehydes, alkanes and alkenes, and high-molecular-weight polycyclic aromatic hydrocarbons (PAH) and PAH derivatives, such as nitro-PA...