Desensitization of ligand-gated ion channels plays a critical role for neuronal signalling. Common GABA_A receptors and glycine receptors show significant desensitization with a time course that depends on receptor subunits and on ligand concentration. The time course of recorded current that is usually taken to represent desensitization may, however, be critically affected by changes in intracellular ion concentrations. Here, I describe an analysis designed to separately estimate the time course of conductance and the changes in intracellular Cl^– concentration, [Cl^–] _i, during activation of native GABA_A- and glycine-receptors in preoptic neurons from rat. In contrast to the prevailing view, it is shown that changes in [Cl^–]_i are critical for the decay of current in the presence of either GABA or glycine while changes in conductance play a minor role only. Conductances decay with time constants of several seconds and in some cells do not decay below the value at peak current, during 20-s agonist application. In contrast to recent reports, it is also shown that apparent cross-desensitization of currents evoked by GABA and by glycine is caused by changes in [Cl^–]_i. By taking the cytosolic volume into account and numerically computing membrane currents and expected changes in [Cl^–] _i, a theoretical framework is provided for the observed effects. Modelling diffusional exchange of Cl^– between cytosol and patch pipettes shows that considerable changes in [Cl^–] _i may be expected and cause rapidly decaying current components in conventional whole-cell or outside-out patch recordings. The findings imply that a re-evaluation of the desensitization properties of GABA_A- and glycine-receptors is needed.