Since its initial description, the pathogenesis of the columnar-lined esophagus (CLE) has been surrounded by many controversies. The first controversy is related to the existence of the condition itself. The second controversy centers on whether the CLE is a congenital or an acquired condition. In this article, we review the congenital and acquired theories of development of CLE and discuss the various factors in acquisition of CLE. The bulk of evidence in the literature suggests that CLE is an acquired condition.