Sensory areas in mammalian cortex compute sensory inputs of different modalities in order to perceive the environment. Much is known about the anatomical pattern of inter-laminar connections, which form the basis of the computational process. Nevertheless, less is known about the functional relevance of these wiring patterns. We used intrinsic optical signals (IOSs) in vitro to investigate functional properties of inter-laminar connections in cortical brain slices of rat sensory cortex. By electrical stimulation in layer VI, a columnar-shaped IOS in all cortical areas was found. We detected different laminar patterns of activation in different cortical areas. In primary sensory areas, like primary visual cortex and primary somatosensory cortex, the peak intensity of IOSs occurred in layer IV, which receives the main thalamic input. In secondary sensory areas, like the secondary visual cortex or the secondary somatosensory cortex, the maximum of IOSs amplitude was shifted to layer II/III. In motor areas, IOS peak amplitude is located in layer II/III. In the hind limb area, considered as amalgam between sensory and motor function, a mixture of the activity patterns observed in primary sensory and a motor area occurred with a peak amplitude in layers II and IV. At different stimulation sites within one cortical area, the shape of columnar IOSs remained very similar, reflecting a canonical architecture of functional micro-circuitry. We conclude that both primary and secondary sensory cortical areas display their characteristic functional activation pattern, regardless of their sensory modalities.