B-cell lymphomas of the gastrointestinal (GI) tract have represented a field of extensive research ever since a close association was shown with chronic inflammatory processes such as Helicobacter pylori infection. Much evidence has accumulated to suggest that the mucosa-associated lymphoid tissue (MALT) induced by inflammation and autoimmune processes is the environment which gives rise to the small cell lymphomas of the GI tract (e.g. extranodal marginal B-cell lymphoma according to REAL). The small B-cell lymphoma may then progress to the large cell variants. Hence, B-cell lymphomas of the GI tract may present a model for lymphomagenesis and progression. In this review, recent cytogenetic data are discussed which yield new insights into the biology of gastrointestinal lymphomas.