Hamartoma of the esophagus is a rare lesion and the number of cases reported in the literature to date is limited. The majority of hamartomas are intraluminal tumors located in the upper third of the esophagus. Histopathologically, the majority of these tumors comprise a mixture of adipose tissue, skeletal/smooth muscle tissue, vascular components and fibrous connective tissue. We herein present the case of a 33-year-old man with an intramural chondroid hamartoma located in the lower third of the esophagus. The patient underwent esophagotomy and the histopathological examination revealed that the tumor was mainly composed of chondroid tissue (60%) admixed with adipose tissue (25%) and fibrous connective tissue (15%). The aim of this study was to describe another variant of esophageal hamartoma, which exhibits a versatile phenotype.