The microstructures of MgB2 wires prepared by the powder-in-tube technique and subsequent hot isostatic pressing were investigated using transmission electron microscopy. Large amount of crystalline defects including small angle twisting, tilting, and bending boundaries, in which high densities of dislocations reside, were found forming sub-grains within MgB2 grains. It is believed that these defects resulted from particle deformation during the hot isostatic pressing process and are effective flux pinning centers that contribute to the high critical current densities of the wires at high temperatures and at high fields.