The functional role of GluR3 AMPA (α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid) receptor subunits has remained elusive. In vitro studies of genetic knockout mice have not yielded significant alterations in synaptic communication. However, behavioural approaches utilizing knockout mice have shown that the subunit may be involved in exploration and motor coordination, suggesting that in vivo methodologies may be more forthcoming. We tested the hypothesis that GluR3 subunits are involved in the modulation of neural network activity. We used a freely behaving mouse model to examine the effect of GluR3–/– on field potential recordings of electroencephalogram, vital functions (i.e. breathing and heart rate) and muscle tone across natural sleep and wakefulness states. We found that GluR3–/– mice virtually lack electroencephalographic signatures of NREM sleep (n = 9) as demonstrated by reduction in electroencephalogram power in the low-frequency bands (δ1, δ2 and θ). In addition, three of nine GluR3–/– mice expressed seizure activity during wakefulness and sleep, suggesting that deletion of the GluR3 gene may predispose to seizure. GluR3 gene knockout also produced state-dependent respiratory modulation, with a selective reduction in breathing rate during behavioural inactivity. These findings show that GluR3 subunits have diverse neurophysiological impact, modulating oscillatory networks for sleep, breathing and seizure generation. Finally, this is the first study to demonstrate the feasibility of direct diaphragm electromyogram recordings in freely behaving mice.