The heteromeric amino acid transporter glycoprotein subunits rBAT and 4F2hc (heavy chains) form, with different catalytic subunits (light chains), functional heterodimers that are covalently stabilized by a disulphide bridge. Whereas rBAT associates with b(0,+)AT to form the cystine and cationic amino acid transporter defective in cystinuria, 4F2hc associates with other homologous light chains, for instance with LAT1 to form a system L neutral amino acid transporter. To identify within the heavy chains the domain(s) involved in recognition of and functional interaction with partner light chains, chimaeric and truncated forms of rBAT and 4F2hc were co-expressed in Xenopus laevis oocytes with b(0,+)AT or LAT1. Heavy chain-light chain association was analysed by co-immunoprecipitation, and transport function was tested by tracer uptake experiments. The results indicate that the cytoplasmic tail and transmembrane domain of rBAT together play a dominant role in selective functional interaction with b(0,+)AT, whereas the extracellular domain of rBAT appears to facilitate specifically L-cystine uptake. For 4F2hc, functional interaction with LAT1 was mediated by the N-terminal part, comprising cytoplasmic tail, transmembrane segment and neck, even in the absence of the extracellular domain. Alternatively, functional association with LAT1 was also supported by the extracellular part of 4F2hc comprising neck and glycosidase-like domain linked to the complementary part of rBAT. In conclusion, the cytoplasmic tail and the transmembrane segment together play a determinant role for the functional interaction of rBAT with b(0,+)AT, whereas either cytoplasmic or extracellular glycosidase-like domains are dispensable for the functional interaction of 4F2hc with LAT1.