Graphene oxide (GO) prepared from graphite powder using a modified Hummers method and reduced graphene oxide (rGO) obtained from GO using different reductants, i.e., sodium borohydride, hydrazine, formaldehyde, sodium hydroxide and L-ascorbic acid, were investigated using transmission electron microscopy, X-ray diffraction, Raman, infrared and electron spectroscopic methods. The GO and rGOs’ stacking nanostructure (flake) size (height x diameter), interlayer distance, average number of layers, distance between defects, elementary composition, content of oxygen groups, C sp³ and vacancy defects were determined. Different reductants applied to GO led to modification of carbon to oxygen ratio, carbon lattice (vacancy) and C sp³ defects with various in-depth distribution of C sp³ due to oxygen group reduction proceeding as competing processes at different rates between interstitial layers and in planes. The reduction using sodium borohydride and hydrazine in contrary to other reductants results in a larger content of vacancy defects than in GO. The thinnest flakes rGO obtained using sodium borohydride reductant exhibits the largest content of vacancy, C sp³ defects and hydroxyl group accompanied by the smallest content of epoxy, carboxyl and carbonyl groups due to a mechanism of carbonyl and carboxyl group reduction to hydroxyl groups. This rGO similar diameter to GO seems to result from a predominant reduction rate between the interstitial layers. The thicker flakes of a smaller diameter than in GO are obtained in rGOs prepared using remaining reductants and result from a higher rate of reduction of in plane defects.