Many pathogenic organisms cause inflammatory lesions and microscopic findings are a useful diagnostic tool for the aetiological diagnosis. However, the histological lesions are limited in respect to many biological agents that can damage the tissues. The histologic hallmark of parasitic diseases is mostly granulomatous inflammation. It is characterized by a focal infiltration of macrophages and epithelioid cells. Many giant cells, lymphocytes, plasma cells, fibroblasts and granulocytes can be found. Agents inducing granulomas include helminths and parasites that replicate intracellularly. Some special stains are utilized in histopathology, for example Giemsa's stain is useful to identify Leishmania. Using specific antibodies, immunohistochemical methods provide an aetiological diagnosis. Sometimes, tissue damage can be immuno-mediated depending on deposit of circulating immunocomplexes or T-lymphocytes involvement rather than by direct parasitic injury. Generally, the lesions which can be observed are respectively vasculitis and inflammatory reactions predominantly composed of mononuclear cells, as observed in many viral or bacterial diseases. In these cases, aetiological diagnosis is improved by in situ-PCR. For microscopic identification of parasites in tissues it is also important to be familiar with the kind of parasites most likely to be found in the examined tissue and in that particular host. Localization of parasites can induce hyperplastic-neoplastic lesions. Many parasites have been associated with the occurrence of specific types of neoplasms, but the mechanisms involved are still not well defined. Chronic inflammation and/or immune suppression seem to induce neoplastic proliferation.