Biodiesel and ethanol are fuels in clear growth and evidence, basically due to its relation with the greenhouse effect reduction. There are several works regarding regulated pollutants emissions, but there is a lack of reports in non-regulated emissions. In a previous paper (Corrêa and Arbilla, 2006) the emissions of aromatic hydrocarbons were reported and in 2007 another paper was published in 2008 focusing carbonyls emissions (Corrêa and Arbilla, 2008). In this work four mercaptans (methyl, ethyl, n-propyl and n-butyl mercaptans) were evaluated for a heavy-duty diesel engine, fueled with pure diesel (D) and biodiesel blends (v/v) of 2% (B2), 5% (B5), 10% (B10), and 20% (B20). The tests were carried using a six cylinder heavy-duty engine, typical of the Brazilian fleet of urban buses, during a real use across the city. The exhaust gases were diluted near 20 times and the mercaptans were sampled with glass fiber filters impregnated with mercuric acetate. The chemical analyses were performed by gas chromatography with mass spectrometry detection. The results indicated that the mercaptans emissions exhibit a reduction with the increase of biodiesel content, but this reduction is lower as the mercaptan molar mass increases. For B20 results the emission reduction was 18.4% for methyl mercaptan, 18.1% for ethyl mercaptan, 16.3% for n-propyl mercaptan, and 9.6% for n-butyl mercaptan.