1 Conflicting reports in the literature over heterogeneity (West et al., 1990) or homogeneity (Arrang et al., 1990) of histamine H-3-receptor binding sites may be attributed to the use of different incubation conditions. In the present study we have investigated the extent to which the binding of H-3-receptor ligands to rat cerebral cortical membranes can be modified by both sodium ions and guanine nucleotides. 2 The H-3-selective antagonist, thioperamide, discriminated between two specific binding sites for [H-3]-N-alpha-methylhistamine (IC50 1 = 2.75 +/- 0.87 nM, IC50 2 = 101.6 +/- 12.0 nM, % site 1 = 24 +/- 2%) in 50 mM Tris HCl buffer, but showed homogeneity of binding in 50 mM Na/K phosphate buffer. 3 Sodium ions markedly altered the binding characteristics of thioperamide (i.e. heterogeneity was lost and IC50 value shifted towards the high affinity site). The competition curves for a second H-3-antagonist, clobenpropit and the H-3-agonist N-alpha-methylhistamine however, were unaltered in the presence of sodium ions. 4 Guanylnucleotides displaced only 60% of specific [H-3]-N-alpha-methylhistamine binding and modulated thioperamide binding in the same way as sodium ions. 5 These data suggest that the H-3-receptor can exist in different conformations for which thioperamide, but not N-alpha-methylhistamine and clobenpropit, show differential affinity. 6 The potential nature of these sites, and the implications of this apparent receptor heterogeneity for H-3-receptor antagonism by thioperamide, are discussed.