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The behavioural activity of freely moving animals is a confounding factor that affects the recording, analysis, and final results of animal EEG experiments. Along with the lack of standardisation in animal in vivo electrophysiology experiments, this could lead to huge inconsistencies, especially in the analysis of centrally acting drugs. Therefore, the main aim of this paper is to investigate the effects of behavioural activity versus inactivity on the multichannel EEG in freely moving rats. In a large sample (n = 116) of waking recordings from 12 cortical electrodes (ECoG) in Wistar rats, we evaluated behavioural activity-related changes in the power spectrum, current source density, and power-based global functional connectivity (GFC) in a 3D rat brain model, according to the TOHOKU Rat Brain Atlas. The main findings were that behavioural activity was associated with 1) a robust power increase in 6-8 Hz, peaking at 7 Hz with maximum changes over the parietal and temporal cortex, 2) an increase in gamma (30-40 Hz) and high-gamma (55-100 Hz) power across the whole brain, 3) a decrease in delta (1-4 Hz) and beta (12-25 Hz) and high-beta (25-30 Hz) power across the whole cortex. Changes were also localised in subcortical regions, particularly in the diencephalon/thalamus. The GFC analysis showed a similar pattern of changes across the 6-8 Hz, delta, and beta bands; however, GFC in the gamma band decreased, while high-gamma GFC increased. Again, the GFC analysis revealed changes in connectivity within subcortical structures, primarily in the thalamus. None of the measures was affected in the alpha band (8-12 Hz). These findings emphasise behavioural state as a critical factor influencing EEG outcomes, with important implications for the standardisation and translational validity of preclinical neurophysiological studies.