We investigated cyanine heterojunction photovoltaic devices using carbocyanine dyes as donors and buckminsterfullerene (C60) as acceptor. In particular, we focused on the influence of cyanine counterions on the photovoltaic device characteristics. It was found that counterions can be displaced in the applied electric field and give rise to important hystereses in the current-voltage characteristics, which are related to charge injection processes at electrode and organic heterointerfaces. Mobile counterions have also a drastic effect on the photocurrent spectrum and are responsible for an important C60 contribution at the organic heterojunction between cyanine and C60. If the counterion is covalently linked to the cyanine dye, the C60 contribution in the blue spectral domain can not be observed.