Six cyanine dyes (including symmetric and unsymmetrical trimethine and pentamethine cyanines with substituted benzoxazolyl or benzothiazolyl groups), were synthesized and evaluated for their in vitro antiprotozoal activities against Plasmodium falciparum K1, Trypanosoma cruzi, T. brucei rhodesiense and Leishmania donovani. Several trimethine cyanines containing benzothiazolyl groups exhibited strong activities against P. falciparum and T. cruzi, whilst one symmetric pentamethine cyanine containing a fluorinated benzothiazolyl group was highly active against T. b. rhodesiense.