Barrett’s esophagus (BE) is defined as metaplastic conversion of esophageal squamous epithelium to intestinalized columnar epithelium. As a premalignant lesion of esophageal adenocarcinoma (EAC), it develops as a result of chronic gastroesophageal reflux disease (GERD). Many studies have been conducted to undertand the molecular mechanism of this disease. This review summarizes recent results of involving squamous transcription factors, intestinal transcription factors, signaling pathways, stromal factors, microRNAs, and other factors in the development of BE. A conceptual framework is proposed to guide future studies. We expect elucidation of the molecular mechanism of BE will help us develop proper management of GERD, BE, and EAC.