The functionality of conjugated polymer systems often relies on oxidations or reductions, in most cases mediated by the presence of counterions. The effect that the common counterion hexafluorophosphate (PF6-) has on the intermolecular interactions between charged oligothiophenes is investigated here using ab initio quantum chemistry methods. Counterions are explicitly included in the simulations of oxidized oligothiophenes and in the dimerization process. Our calculations provide quantitative and qualitative insight into the intermolecular interactions in oligothiophene-counterion systems and show that the intermolecular pi-stacking of oligothiophenes is not adversely affected by the presence of counterions and that in fact oligothiophene dimerization is further stabilized by their presence.