The effect of counterions on the properties and structure of conducting polymers was studied by using a series Of Cl-3(-) doped polythiophenes (PTs) as a case example. Hybrid density functional theory (DFT) with periodic boundary conditions (PBC) at the B3LYP/6-31G(d) level has been used. This is the first theoretical study of infinitely long doped PT using DFT with counterions explicitly taken into account. The balance between charge carrier states was addressed by studying the singlet and triplet state unit cells of differently doped PTs. The relative isomer energies, density of states diagrams, bond length alternation, and charge distribution patterns were analyzed. Interestingly, the position of the counterion is flexible over the polymer chain and the electronic structure of the polymer and, consequently, optical properties are sensitive to the position of the counterion. A bipolaron electronic configuration is preferred at high dopant concentrations (one dopant per six or less thiophene rings) while a polaron pairs configuration is preferred at low dopant concentrations (one dopant per ten or more thiophene rings) which is in line with many experimental observations.