Poly(3-hexylthiophene) synthesized by chemical oxidation with FeCl3 was investigated with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using either dithranol or the electron-transfer matrices terthiophene and anthracene. Two to three series of ions were observed in the MALDI mass spectra. These series all have hexylthiophene repeat groups, and the end groups/modifications were identified as two or more chlorine atoms through the analysis of isotopic distributions and exact mass measurements. The chlorine atoms may be end groups (on alpha- or beta -carbons of terminal thiophenes) or substituents on the beta -carbons of the thiophene groups along the polymer backbone. Although poly(3-alkylthiophenes) synthesized by this method have been reported to contain iron or chlorine impurities, this is the first demonstration that the polymeric product actually contains chlorine atoms that are covalently bound to the polymer chain (vs residual FeCl3). The FeCl3 oxidizing agent-not the chlorinated solvent-is found to be responsible for halogenating the polymer, as determined by experiments with FeBr3 as the oxidant. In addition, we have demonstrated that when using either dithranol or the electron-transfer matrices, the ion series represent radical molecular cations, Mcircle+, rather than the protonated molecules or salt adducts that are typically observed in XL LDI-MS.