We report for the first time in the Philippines a case of portal vein thrombosis in a 12 year old Filipino boy with advanced schistosomiasis. The boy was referred to the Research Institute for Tropical Medicine (RITM), Manila, due to a rapidly enlarging spleen post-praziquantel treatment. At RITM, liver function tests were within normal limits but complete blood examinations showed pancytopenia and abnormal coagulation times. Serum markers for hepatitis A, B and C were negative. Abdominal MRI revealed schistosome-induced periportal fibrosis. The main portal vein appeared thrombosed with characteristic cavernous transformation of the right portal vein. Varices were seen in the oesophagus, gastrohepatic ligament, and splenic hilum. The spleen was markedly enlarged, with parenchymal foci representing Gamna-Gandy bodies. The patient underwent splenectomy. Histopathologic findings in the liver showed moderate pipestem fibrosis and schistosome egg granulomas. The patient was discharged from the hospital in excellent clinical condition.