We examined the biological reactivity in vitro of nanoparticles of organic compounds (NOC) with diameters, d = 1-3 nm, a class of combustion-generated particulate relatively unstudied compared to larger more graphitic soot particles because of their small size even though they may contribute significantly to the organic fraction of PM sampled from vehicle exhausts and urban atmospheres. We tested NOC samples collected from 2004 model vehicle emissions and laboratory flames. NOC produced a dose dependent mutagenic response in Salmonella bacteria, suggesting that NOC may add significantly to the overall mutagenicity of vehicle emissions. Incubation with peptides caused agglomeration and precipitate of the otherwise stable NOC suspension, but the chemical and/or physical nature of the NOC-peptide interactions could not be resolved. A significant cytotoxic response was measured above a critical dose of NOC in mouse embryo fibroblasts NIH3T3 cells along with possible evidence of cellular uptake by optical and confocal microscopy. The toxicological assays showed that NOC collected from flames and vehicle exhausts effectively interacted in vitro with both prokaryotic and eukaryotic cells. Differences in mutagenic potencies observed for various Salmonella strains with and without metabolic activation indicate differences in the chemical composition of NOC collected from different vehicles and flames.