We report immunohistochemical (IHC) and molecular findings in a rare case of a carcinoid tumor of the extrahepatic bile ducts in a 33-year-old woman, who presented with a 3.9x2.8x2.6 cm mass within the right and common hepatic ducts. She underwent surgery and a carcinoid tumor was identified. This lesion is of interest because in addition to the morphological and cytological features of a typical carcinoid, it demonstrated a distinct pleomorphic area immunoreactive for gastrin. By molecular analysis, loss of heterozygosity (LOH) with opposite allelic patterns between the gastrin-positive and gastrin-negative areas of the tumor was identified. The molecular studies for LOH along with the morphology and IHC profiling suggest that this second population of gastrin-positive carcinoid cells may represent a new clone within the carcinoid tumor with differentiation toward gastrin production or may represent the next step in the carcinogenic process with a gradual emergence of a more aggressive clone.