Cortical dysplasias frequently underlie neurodevelopmental disorders and epilepsy. Rats with a neonatally induced cortical microgyrus [freeze-lesion (FL)], a model of human polymicrogyria, display epileptiform discharges in vitro. We probed excitatory and inhibitory connectivity onto neocortical pyramidal neurons in layers 2/3 and 5 of postnatal day 16-22 rats, approximately 1-2 mm lateral of the lesion, using laser scanning photostimulation (LSPS)/glutamate uncaging. Excitatory input from deep and supragranular layers to layer 5 pyramidal cells was greater in FL cortex, while no significant differences were seen in layer 2/3 cells. The increased input was due to a greater number of LSPS-evoked excitatory postsynaptic currents (EPSCs), without differences in amplitude or kinetics. Inhibitory input was increased in a region-specific manner in pyramidal cells in FL cortex, due to an increased inhibitory postsynaptic current (IPSC) amplitude. Connectivity within layer 5, parts of which are destroyed during lesioning, was more severely affected than connectivity in layer 2/3. Thus, we observed 2 distinct mechanisms of altered synaptic input: 1) increased EPSC frequency suggesting an increased number of excitatory synapses and 2) higher IPSC amplitude, suggesting an increased strength of inhibitory synapses. These increases in both excitatory and inhibitory connectivity may limit the extent of circuit hyperexcitability.