A new screening method has been explored for direct analysis of tobacco smoke biomarkers in biological matrices (i.e., saliva and urine). Single run analysis using Atmospheric pressure Solid Analysis Probe (ASAP) and high resolution mass spectrometry with quadrupole and time of flight detector has been applied directly to some biological samples (i.e., urine and saliva), providing a fast, efficient and sensitive method of identification. The method has been applied to saliva and urine samples from heavy tobacco smokers for exposure studies. Nicotine itself, nicotine metabolites (i.e., cotinine, trans-3′-hydroxycotinine, nicotine-N-glucuronide) and other related tobacco smoke toxic compounds (i.e., NNK 4-[methyl(nitroso)amino]-1-(3-pyridinyl)-1-butanone, anatabine) were found in the analyzed samples. The identification of compounds was confirmed by ultrahigh performance liquid chromatography with MS-triple quadrupole detector after sample treatment. Different temporal trends and biomarkers behavior have been found in time series related samples. Both methods are compared for screening of these biological matrices.