This review is part two of three, which will present an update on the classification of gastrointestinal submucosal tumors. Part one treats of the diagnosis and part three of the therapeutic methods regarding gastrointestinal submucosal tumors. In the past there has been some confusion as to the classification of gastrointestinal submucosal tumors. Changes in classifications have emerged due to recent advances in mainly immunohistochemistry and electron microscopy. The aim of this paper is to update the reader on the current classification. Literature searches were performed to find information related to classification of gastrointestinal submucosal tumors. Based on these searches the twelve most frequent submucosal tumor types were chosen for description of their classification. The factors that indicate whether tumors are benign or malignant are mainly size and number of mitotic counts. Gastrointestinal stromal tumors are defined mainly by their CD117 positivity. In the future, there should be no more confusion between gastrointestinal stromal tumors and other types of submucosal tumors.2007 The WJG Press. All rights reserved. This review is part two of three, which will present an update on the classification of gastrointestinal submucosal tumors. Part one treats of the diagnosis and part three of the therapeutic methods regarding gastrointestinal submucosal tumors. In the past there has been some confusion as to the classification of gastrointestinal submucosal tumors. Changes in classifications have occurred due to recent advances in mainly immunohistochemistry and electron microscopy. The aim of this paper is to update the reader on the current classification. Literature searches were conducted to find information related to classification of gastrointestinal submucosal tumors. Based on these searches the twelve most frequent submucosal tumor types were chosen for description of their classification. The factors that indicate that tumors are benign or malignant are mainly size and number of mitotic counts. Gastrointestinal stromal tumors are defined mainly by their CD117 positivity In the future, ther e should be no more confusion between gastrointestinal stromal tumors and other types of submucosal tumors. 2007 The WJG Press.