Multiplicity of oscillatory phenomena in a range of infra-slow frequencies (<0.01 Hz) has been described in mammalian brains at different levels of organisation. The significance and manifestation in physiology and/or behaviour of many brain infra-slow oscillations (ISO) remain unknown. Examples of this phenomenon are two types of ISO observed in the brains of urethane-anaesthetised rats: infra-slow, rhythmic changes in the rate of action potential firing in a few nuclei of the subcortical visual system and a sleep-like cycle of activation/deactivation visible in the EEG signal. Because both of these rhythmic phenomena involve brain networks that can influence autonomic nervous system activity, we hypothesised that these two brain ISOs can be reflected by rhythmic changes of pupil size. Thus, in the present study, we used simultaneous pupillography and ECoG recording to verify the hypothesised existence of infra-slow oscillations in the pupil size of urethane-anaesthetised rats. The obtained results showed rhythmic changes in the size of the pupils and rhythmic eyeball movements in urethane-anaesthetised rats. The observed rhythms were characterised by two different dominant components in a range of infra-slow frequencies. First, the long component had a period of ≈29 minutes and was present in both the irises and the eyeball movements. Second, the short component had a period of ≈2 minutes and was observed only in the rhythmic constrictions and dilations of the pupils. Both ISOs were simultaneously present in both eyes, and they were synchronised between the left and right eye. The long ISO component was synchronised with the cyclic alternations of the brain state, as revealed by rhythmic changes in the pattern of the ECoG signal. Based on the obtained results, we propose a model of interference of ISO present in different brain systems involved in the control of pupil size.