A comparative mass spectral examination of the trimethylsilyl (TMS) derivatives of 2'-, 3'- and 5'-deoxyadenosine, 2'-, 3'- and 5'-deoxyguanosine, 2'-, 3'- and 5'-deoxyxanothosine and 2'- and 5'-deoxy-2-fluoroadenosine is presented. A general compilation of the major fragment ions found in the low-resolution electron ionization (EI) spectra of the eleven deoxynucleosides is given. Chemical ionization (CI)-collisional activation (CA) daughter ion spectra are reported using the deoxyadenosines as model compounds. Ion structures and fragmentation pathways are proposed for those ions characteristic of each of the isomers. Significant differences in fragmentation exist between the isomeric 2'-, 3'- and 5'-purine deoxynucleosides. The formation and structures of ten ions important in this differentiation are discussed. The CI-CA linked scan spectra provide complementary structural information relative to the EI mass spectra.