In the Mediterranean region Leishmania infantum causes both visceral and cutaneous leishmaniasis. These two pathologies tend to be caused by distinct parasite zymodemes. We have studied 33 isolates of Leishmania, 2 from sandflies, 5 from visceral cases, and 26 from cutaneous cases in Honduras, to determine if there is a correlation between pathology and parasite type in the New World similar to that in the Mediterranean region. Nine of the 26 cutaneous cases were caused by L. mexicana parasites, which have not been previously reported from Honduras; the remaining 17 cutaneous cases were due to L. chagasi. Only minor differences were found between the Honduran L. chagasi parasites by random amplified polymorphic DNA, differential display, pulsed-field gel electrophoresis, and schizodemes. This suggests that in Honduras the parasite type may not be the only factor determining the clinical outcome of L. chagasi infections.