Background: Mast cells produce a number of lymphokines and chemokines upon Fc epsilon RI stimulation. However, signal cascades and transcription factors involved in the induction of the corresponding genes are still poorly understood. Methods: We addressed this issue using transient transfections of a TNF alpha promoter-driven reporter gene and corresponding 5' successive deletions, the two phosphoinositol-3 kinase inhibitors demethoxyviridin and wortmannin, ELISAs and Western and Southwestern blots. Results: Nuclear factor of activated T cells (NF-AT) and AP1 transcription factors together mediate the activation of TNF alpha transcription in mast cells upon IgE plus antigen stimulation which, in contrast to the degranulation reaction and leukotriene synthesis, is independent of phosphoinositol-3-kinase. Conclusions: TNF alpha regulation in mast cells provides an experimental system for direct comparison of the regulation of this cytokine in T cells. In the context of our recent findings on IL-5 gene regulation in mast cells, a picture emerges in which NF-AT, dependent on the cytokine and not on cell type, interacts with a specific cofactor (AP1 for TNF alpha, GATA for IL-5). Multiple NF-AT family members found to be expressed in mast cells provide the structural basis for these different interactions with cofactors. The insensitivity of TNF alpha gene activation and release to inhibitors of phosphoinositol-3 kinase demonstrates that the activation of NF-AT and/or AP1 transcription factors in mast cells is not triggered along this signaling cascade.