Abstract Rationale Human high affinity receptors for IgE, FcεRI, are expressed as two isoforms: αβγ2 on mast cells and basophils and αγ2 on antigen presenting cells. Murine FcεRI is only expressed as αβγ2 isoform and its surface expression requires the β chain. As a first step to create humanized FcεRI mouse models, we analyze the molecular basis that underlies β-chain dependency/independency for murine/human FcεRI expression. Methods Sequence alignment and structural comparisons were done and human α extracellular region 3-D structure was compared to a model of mouse α extracellular region. Several candidate regions were selected to generate different chimeric proteins. The chimeric proteins were cotransfected with either β and γ subunits or with γ subunits alone and FcεRI cell surface expression was analyzed. Results Our data indicate that the extracellular region of the human α chain allows αγ2 complex expression, but that the mouse α extracellular region permits only αβγ2 expression. Therefore, structural comparisons of these extracellular regions provided a basis to explore this difference. Several residues located in two loops BC and C'E, in D1 domain of the α chain extracellular region were identified and chimeric molecules were constructed to express these differing residues. Our studies revealed that these structural differences are not solely responsible for the murine β chain dependency. Importantly, our studies indicate that both loops are required for optimal FcεRI expression. Conclusion The β chain dependency/independency in the mouse/human FcεRI expression is derived from information that is contained in the α chain extracellular region.