We report the results of molecular dynamics studies on the stability of different triple helices containing the pyrimidine motif d(G.C.C) in aqueous solution. The stability of triplexes where the Hoogsteen cytosine is protonated is compared with that of triplexes where the same base is present as the neutral imino tautomer. Results support the hypothesis that Hoogsteen cytosines in triplexes where d(G.C.C) trios are contiguous are not fully protonated, but a certain percentage of neutral form exists. The results help in the understanding of the apparently contradictory experimental data on d(G.C.C)-containing triplexes, and encourages new studies in the field.