A promising way to elucidate neuronal information processing is to establish detailed structure-function relationships of identified single neurons or populations of nerve cells, especially their synaptic connectivity. This has been greatly improved by the development of acute brain slice preparations. The cellular physiology of the rodent primary somatosensory (barrel) cortex has been extensively studied. However, for a meaningful interpretation of physiological experiments the degree and pattern of connectivity has to be known for the particular preparation. Since such studies are not available for rat (P15-25) barrel cortex in vitro, we have traced the cortico-cortical and thalamo-cortical connections in 400-microm-thick slices with biocytin. In coronal slices, a wealth of axonal connections in retrograde and anterograde directions were heavily labeled, resembling the full pattern of cortico-cortical projections described in vivo. The most striking connections were vertical and horizontal connections within the primary somatosensory cortex, as well as a columnar projection to the secondary somatosensory cortex and beyond (mainly the parietal ventral area). Electron microscopic extensions of the study indicated that the full possible set of synaptic contacts with an adult-like appearance was already established in these connections. In thalamo-cortical slices, strong reciprocal connections with the ventrobasal (and to a much lesser extent also the posterior) thalamic nucleus were always observed, together with an intensive ramification of fibers in the reticular nucleus. A striatal terminal field was also consistently found. We conclude that all major intracortical and thalamo-cortical connection are richly preserved in the in vitro slice preparations of rats. Thus, these preparations are suitable for elucidation of the functional interaction of the most crucial brain structures involved in somatosensory information processing combining an in vivo-like anatomical structure with the controlled environment of an in vitro slice.