We have previously reported that patients suffering from atopic dermatitis (AD) frequently display IgE autoantibody reactivity to human proteins expressed in cell lines of different histogenetic origins. Molecular cloning and in situ staining experiments revealed that certain IgE-reactive autoantigens were expressed preferentially in target organs of atopy while others could be detected in various tissues and cell types. Here we use serum IgE from AD patients to investigate the distribution of autoantigens in subcellular fractions of the human epithelial cell line A431 and in human tissue specimens. Results obtained showed that IgE-reactive autoantigens can be detected in the nuclear > microsomal > mitochondrial > cytoplasmic fraction of A431 cells as well as in a variety of human tissue specimens (brain, bone, intestine, liver, lung, muscle, skin, uterus) and effector cells of atopy (basophils, mast cells, T cells). If IgE autoreactivity plays a pathogenetic role in severe forms of atopy, organ-specific manifestations (e.g. AD) may result from the transport to and deposition of IgE-reactive autoantigens in certain target organs (skin) rather than from a preferential expression of the autoantigens in the affected tissues.