The histopathologic investigation of children with congenital immunodeficiency, and its relation to functional parameters and clinical data have been a major contribution to the present knowledge on the histophysiologic aspects of normal immune system function. Based on thorough knowledge in histophysiologic and dynamic aspects of lymphoid organs, the histopathologic evaluation in cases of suspected immunodeficiency today forms an integral part of the assessment of the immune status. Apart from conventional histologic techniques, advanced technology such as immunohistochemistry and in situ hybridization is applied. This enables analysis of the basic cellular components in various lymphoid tissue compartments, and evaluation of the consequences of the deficiency by the assessment of microorganisms and neoplasia. This review focuses on the histopathologic contribution to immunodeficiency evaluation. Sections deal with (1) the description of alterations in the various lymphoid tissues (bone marrow, thymus, lymph node, spleen, and gastrointestinal tissue); (2) histopathology of infection and malignancy; (3) pathology of some types of congenital immunodeficiency; (4) histopathologic methods and reagents; and (5) an autopsy protocol for immunodeficiency.