Upstream gene structure and mRNA expression of the human histamine H1 receptor gene was investigated in cells relevant to the pathogenesis of asthma, (primary cultured human airway smooth muscle cells, primary cultured bronchial epithelial cells and BEAS2B cells), and other tissues known to express histamine H1 receptors (placenta and brain). Splice variation of the 5' terminal exons gave three separate locations for novel promoters upstream of the detected transcription start sites. Further splice variants in the 5' untranslated region were also observed. Transient transfections of promoter/luciferase constructs showed these regions directed expression in human airway smooth muscle cells and BEAS2B cells. Polymorphism screening of the major regulatory regions identified a number of novel SNPs. Expression of splice variants was confirmed by real-time PCR assays. Results showed one 5' terminal exon splice variant, comprising exons B/K, expressed preferentially in all tissues. Interestingly the other 5' terminal exon splice variants showed tissue-specific patterns of expression, with variant F/K expressed negligibly (0.1%) in human airway smooth muscle cells but accounting for 19.3% and 8.3% of total expression in BEAS2B cells and differentiated human bronchial epithelial cells. Splice variant A/K was second most highly expressed in differentiated human bronchial epithelial cells (23%) whereas its expression in BEAS2B and human airway smooth muscle cells was 1.7 % and 4.4% respectively. These data suggest the use of alternative promoters directing human H1 receptor gene expression, both within and between cell types.