Histologic examination of lymphoid organs has revealed immunotoxic effects of a broad range of substances. The thymus has proven especially sensitive. The relative lack of sensitivity of mucosa-associated lymphoid cells and tissues may be due to shortcomings in the way they are examined. Validation of ways to examine mucosal lymphoid tissues and cells and development of histopathological tools to flag a compound as a potential inducer of autoimmune disease or allergy are challenges for the future. © 2006 Elsevier GmbH. All rights reserved.