Although the first clinical description of Langerhans cell histiocytosis (LCH) was published over a century ago, the aetiology and pathogenesis of this enigmatic disorder are still remained unknown. Viral, immunological, neoplastic and other pathogenetic mechanisms have been considered, but none has been proven. The prevailing opinion is that LCH is a reactive disorder rather than a neoplastic process, but this presumption has never been definitively tested. A key feature of a neoplasm is its clonal derivation from a single cell. To determine if LCH is a polyclonal reactive or a clonal disorder, we and others have recently used molecular biological techniques to assess clonality in LCH. Using X chromosome-linked DNA probes that can detect clonal or polyclonal X chromosome inactivation patterns in female tissues, clonal CD1a+ histiocytes have now been detected in the lesional tissues in each of 16 females affected with LCH. Most of these patients were studied prior to the initiation of therapy. Lymphoid clonality was excluded in all cases in which it was studied, confirming that the clonal cells in LCH are the CD1a+ dendritic cells presumed to be pivotal in this disorder. Two distinct lesions (a pre-treatment bone biopsy and a lymph node biopsied 3 years later) have been studied in only one case to date; the same clonal pattern of X chromosome inactivation was observed, consistent with persistence of the same clone during this patient's disease course.(ABSTRACT TRUNCATED AT 250 WORDS)