In this paper, attempts to dope polypyrrole (PPy) with two small sized anionic drugs, diclofenac sodium salt (NaDF) and valproic acid sodium salt (NaVPA), are described. For PPy doped with DF−, unusual patterns in growth and morphology were observed. During the deposition of the polymer, the rate of electropolymerisation decreased with increasing time and higher applied potentials. The polymer had features of an insulating film, while SEM confirmed the presence of crystal-like shards on the surface of the polymer. Analyses of these crystals indicate them to be drug that may have precipitated out of solution. These findings suggest that insoluble drug crystals are formed during electropolymerisation. The formation of PPy doped with a small soluble anti-epilepsy anionic drug, VPA−, was also studied; however it was not possible to incorporate this drug during electrochemical polymerisation. Again, this was explained in terms of the equilibrium between the anion and the acid forms of VPA. At pH values below 5.6, the equilibrium of the VPA− is shifted towards the insoluble HVPA. As the monomer is oxidised, there is a decrease in the local pH in the vicinity of the electrode and this causes the HVPA to precipitate from solution. This, in turn, prevents any PPy from being deposited at the electrode.