Malaria is no longer endemic in Puerto Rico, however, imported cases of the disease are occasionally reported to the Health Department of the Island. This is a report of a 45-year-old female patient who traveled to Kenya and Niger and was admitted to a San Juan area hospital with an 8 day history of daily chills and fever, myalgia, nausea and vomiting. Upon admission, peripheral blood displayed multiple intra-erythrocytic ring-shape trophozoites, highly suggestive of Plasmodium falciparum. The polymerase chain reaction was used as a complementary method for the detection of malaria parasites and confirmation of post-treatment parasite clearance. This report presents an imported case of malaria in Puerto Rico and showed the use of a molecular technique to diagnose Plasmodium.