Transient receptor potential vanilloid 1 (TRPV1) is a tetrameric non-specific cation channel consisting of 6 transmembrane (TM) domains. In canine brain and breast cancer AZACB cells, we found the expression of a full-length (F) as well as a splice isoform (T) missing the first TM (TM1) and a part of the second TM (TM2) domains. We investigated whether the lack of this region in any subunit generating tetramers may affect the channel function. Ca²⁺ imaging experiments were conducted using Fura-2 in AZACB cells or HEK293 cells that were transfected with each of F and T monomers, or with one of the concatemers composed of the two subunits (FF, TT, FT and TF). Western blot and immunocytochemistry confirmed the expression of these channels in the transfected cells. Capsaicin, a TRPV1 stimulator, potently increased [Ca²⁺]_i in the F- or FF-transfected cells in a concentration-dependent manner, while it exhibited a smaller [Ca²⁺]_i increase in T-, TT-, FT- and TF-transfected cells. The cells expressing the T-containing heteromers as well as AZACB cells exhibited the greater cell variability of the Ca²⁺ response. Therefore, the formation of heteromeric TRPV1 including the variant lacking TM1 and a part of TM2 appeared to modify the channel function.