The morphologic classification of thymoma has undergone numerous revisions in recent years and has been under continuous debate for the past several decades. With the introduction of the World Health Organization (WHO) schema for the classification of thymic epithelial neoplasms in 1999, a major step was taken toward achieving uniformity in the nomenclature of these tumors. A more recent iteration of the WHO morphologic classification of thymic epithelial neoplasms has now been published. Although these efforts have certainly contributed to clarifying many issues related to the pathology of thymoma, several problem areas and inconsistencies still remain surrounding this proposed schema. The purpose of this review is to address these problem areas, in particular as it relates to terminology, histopathologic criteria for diagnosis, and the prognostic significance for the various categories of the WHO schema.