Cyclic nucleotide-gated (CNG) channels are tetrameric non-specific cation channels. They mediate the receptor potentials in photoreceptors and cells of the olfactory epithelium and they are activated by the binding of cyclic nucleotides such as cGMP and cAMP. Previous studies in homotetrameric CNGA1 channels, activated with covalently bound cGMP, presented evidence that partially liganded channels cause partial channel opening (Ruiz & Karpen, 1997, 1999). Here, homotetrameric CNGA1 channels were expressed in Xenopus oocytes. Conductance and gating of these channels were studied as a function of the concentration of freely diffusible cGMP and with different permeating ions. At saturating cGMP the current levels distributed around a single mean in a Gaussian fashion and the open times were long. At low cGMP, however, the current levels were heterogeneous: they were smaller than those at saturating cGMP, equal, or larger. The open times were short. Ions generating the larger single-channel currents (Na(+) > K(+) > Rb(+)) concomitantly increased the heterogeneity of current levels and decreased the open probability and open times. The results suggest that the activation of CNGA1 channels by cGMP and ions staying longer in the pore is associated with less extensive and less frequent conformational fluctuations of the channel pore.