Membrane transport proteins play a central role in many biological processes by mediating the transport of many different solutes, such as ions, nutrients, and neurotransmitters across biological membranes. Numerous pathological conditions result from impairments in the function of molecules of this class.Many prokaryotic and eukaryotic Na+-driven transporters couple the movement of one or more Na+ ions down their electrochemical gradient to the active transport of a variety of solutes. When more than one Na+ is involved, Na+ binding data are usually analyzed using the Hill equation with a non-integer exponent n. The results of this analysis are an overall Kd-like constant and n, a measure of cooperativity. This information is usually insufficient to provide the basis for mechanistic models. In the case of transport utilizing two Na+ ions n < 2 indicates that molecules with only one of the two sites occupied is present at low saturation. Here we propose a new way of analyzing Na+ binding data for the case of two Na+ ions that, by taking into account binding to individual sites, yields bounded ranges of pairs of possible values for the Na+ affinities of the individual sites. These values provide far more information than can be obtained by using the Hill equation with a non-integer coefficient.To illustrate the advantages of the new analysis we used experimental data on Na+ binding to the Na+/I- symporter (NIS)—the key protein that mediates the first step for the biosynthesis of the thyroid hormones—obtained by scintillation proximity assay (SPA). The same formalism can be used to analyze data of other proteins that bind the same substrate at two binding sites.