Background Deep eosinophilic granulomatous abscesses, as distinguished from eosinophilic subcutaneous abscesses, are rare. Most reports are from the Far-East and India where the most commonly attributed cause is Toxocara. Sulaimaniyah in Northeastern Iraq has experienced an outbreak of eosinophilic granulomatous liver and gastrointestinal (GI) abscesses beginning in 2009. The purpose of this study was to determine the etiology and guide treatment. Methods The study was an ongoing investigation of patients having a histopathologic diagnosis of eosinophilic granulomatous abdominal abscesses in Sulaimaniyah hospitals from May 2009 to August 2012. Tissues were examined for organisms, and Enzyme Linked Immunoabsorbent Assays (ELISA) were performed for serum antibodies to Fasciola hepatica, Toxocara, and Echinococcus granulosus. Results Fourteen patients had granulomatous inflammation surrounding a central necrotizing eosinophilic exudate identified in surgical pathology specimens from abdominal surgeries. Two children and four adults had abscesses that formed GI masses. These patients included a 39 year old male with oropharyngeal and transverse colon disease, and a 48 year old male with liver and GI abscesses. All sites demonstrated a Zygomycete fungus surrounded by eosinophilic Splendori-Hoeppli material consistent with basidiobolomycosis. Five of the six patients with fungal disease were treated by surgery and 4 to 7 months of itraconozol. One child died of intestinal perforation while receiving IV amphotericin B; two adults required additional surgery for recurrent GI obstruction. Eight patients had isolated liver abscesses with no organisms identified by histopathology: ELISA results for F. hepatica were positive for five, borderline for one, and negative for two patients. These eight patients were treated for fascioliasis by surgical resection of localized abscesses and albendazol. One patient serologically positive for F. Hepatica was found to have a common duct fluke two years after initial diagnosis. Serological testing for Toxocara and Echinococcus granulosus was negative in all 14 patients. Conclusions Basidiobolomycosis and F. hepatica are implicated as the cause of abdominal eosinophilic granulomatous abscesses in 12 of 14 patients identified over a period of 40 months in northern Iraq. Treatment was complicated by chronic biliary tract disease in fascioliasis and perforation and recurrent intestinal obstruction with basidiobolomycosis.