We describe a method for imaging the local cortical haemodynamic response to whisker stimulation in the rat without use of anaesthetic or paralytic agents. Female Hooded Lister rats were anaesthetised and a section of skull overlying somatosensory cortex thinned to translucency. A stainless steel chamber was then secured over the thin cranial window. Following recovery, animals were supported in a harness whilst the head was held by the implanted chamber using a pneumatically driven clamp. Optical imaging and optical imaging spectroscopy (OIS) of somatosensory cortex were performed whilst the contralateral whiskers were stimulated using a computer controlled air-puffer. Imaging sessions lasted approximately 15 min and data were collected for at least three consecutive days. Experiments were then repeated with the animals under urethane anaesthesia. Spectral analysis revealed qualitatively similar haemodynamic response functions across both anaesthetic states. However, our results indicate that the cortical haemodynamic response to somatosensory stimulation is larger by a factor of approximately 5 in the unanaesthetised rat compared with the anaesthetised rat. This preparation may make possible the investigation of the haemodynamic correlates of a broad range of neurological processes in the awake, behaving rodent.