ClC-3, a member of the large superfamily of ClC voltage-dependent Cl- channels, has been proposed as a molecular candidate responsible for volume-sensitive osmolyte and anion channels (VSOACs) in some cells, including heart and vascular smooth muscle. However, the reported presence of native VSOACs in at least two cell types from transgenic ClC-3 disrupted (Clcn3-/-) mice casts considerable doubt on this proposed role for ClC-3. We compared several properties of native VSOACs and examined mRNA transcripts and membrane protein expression profiles in cardiac and pulmonary arterial smooth muscle cells from Clcn3+/+ and Clcn3-/- mice to: (1) test the hypothesis that native VSOACs are unaltered in cells from Clcn3-/- mice, and (2) test the assumption that targeted inactivation of the Clcn3 gene using a conventional murine global knock-out approach results in the exclusive elimination of the targeted protein. Our experiments demonstrate that VSOAC currents in myocytes from Clcn3+/+ and Clcn3-/- mice are remarkedly similar in terms of activation and inactivation kinetics, steady-state current densities, rectification, anion selectivity (I- > Cl- >> Asp-) and sensitivity to block by glibenclamide, niflumic acid, DIDS and extracellular ATP. However, additional experiments revealed several significant differences in other fundamental properties of native VSOACs recorded from atrial and smooth muscle cells from Clcn3-/- mice, including: differences in regulation by endogenous protein kinase C, differential sensitivity to block by anti-ClC-3 antibodies, and differential sensitivities to [ATP]i and free [Mg2+]i. These results suggest that in response to Clcn3 gene deletion, there may be compensatory changes in expression of other proteins that alter VSOAC channel subunit composition or associated regulatory subunits that gives rise to VSOACs with novel properties. Consistent with this hypothesis, in atria from Clcn3-/- mice compared to Clcn3+/+ mice, quantitative analysis of ClC mRNA expression levels revealed significant increases in transcripts for ClC-1, ClC-2, and ClC-3, and protein expression profiles obtained using two-dimensional polyacrylamide gel electrophoresis revealed complex changes in at least 35 different unidentified membrane proteins in cells from Clcn3-/- mice. These findings emphasize that caution needs to be exercised in simple attempts to interpret the phenotypic consequences of conventional global Clcn3 gene inactivation.