Aim: Synapses play a key role in signal processing in the brain. Individual input synapses, on physiologically and morphologically characterised early postnatal layer 4 (L4) spiny neurons, were 3D reconstructed to analyse the structural composition. Methods: Excitatory L4 neurons in the rat barrel cortex were patched and filled with biocytin. The labelled neurons were reconstructed with Neurolucida (MicroBrightField, Colchester, VT). Serial ultrathin sections of the patched neurons were cut and photographed using an electron microscope; the images were subsequently imported into the reconstruction software CAR. Labelled dendrites and all input synapses with vesicles, active zones and mitochondria were outlined. From contours three-dimensional volumetric reconstructions were performed and structural determinants like vesicle number calculated. Results: In a six-days-old rat 13 input synapses of a L4 spiny neuron were reconstructed. One of them was located on the soma and the remainder on the proximal dendrites. Most boutons possess a single active zone, but for three boutons a second active zone was found. Boutons varied in shape and size, ranging from 1.5 mm² surface area to 13 mm², a nearly 10-fold difference. As well, the number and size of vesicles differed between the synapses, 22-469 per bouton and 17-84 nm, respectively. Conclusion: The observed number of vesicles is low, indicating that the synaptic transmission in this young rat is not very effective. Probably, the readily releasable pool in L4 spiny neurons diminishes fast suggesting that this synaptic connection is not as reliable as in the mature neocortex.