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A 15-year-old female patient presented with numerous, small, papulonodular skin lesions, and hepatosplenomegaly 9 months after a treated biopsy proved cutaneous leishmaniasis. In ocular examination there were two yellowish, raised gelatinous conjunctival lesions in the left eye. The exisional conjunctival lesion biopsy revealed many Leishman bodies inside tissue histiocytes. The patient had no systemic immunologic problems (normal serum immunoglobulins, nitroblue-tetrazolium test, complement CH50 test and flow cytometry of leukocytes). The indirect immunofluorescent antibody test for Leishmania tropica (titre of 1:1024) and the leishmanin skin test were positive. DNA of L. tropica was detected by a specific polymerase chain reaction on whole blood, bone marrow and skin biopsy specimens. The skin and conjunctival lesions disappeared with miltefosine and no intraocular tissue penetration of organism happened. Conjunctival leishmaniasis should be considered in the differential diagnosis of raised conjunctival lesions in a disseminated cutaneous leishmaniasis patient and needs proper systemic therapy.