The development of nanoclay-epoxy nanocomposite material requires a suitable blending process to be employed. Amongst blending techniques, sonication has been one of the promising means for polymer-clay nanocomposite fabrication. In this study, epoxy-clay nanocomposites with 2, 4 and 5% clay loadings were fabricated using different sonication periods ranging from 5 to 60 minutes. The effect of sonication time and clay loading on the nanocomposite structure was investigated using Differential Scanning Calorimetry (DSC), X-ray diffraction (XRD), Scanning Electron Micropscope (SEM) and Energy Dispersive Spectroscopy (EDS). Differential Scanning Calorimetry analysis indicated that while clay loading reduced the glass transition temperature (Tg), sonication time did not alter Tg significantly. Upon examining the structure of the resulting nanocomposites both exfoliation and intercalation structures were present, yet, neither structure was fully achieved; evident by the XRD patterns. Nonetheless, the predominant structures for most of the nanocomposites were intercalation. Intergallery spacing of the nanocomposites were enhanced with increased sonication time mainly at 2%wt loading; whereas further increase in nano-clay loading resulted in a reduction of the d-spacing. SEM analysis showed that clay agglomerates were present in the nanocomposites irrespective of the sonication time. However, the analysis revealed that dispersion of clay was better in the nanocomposite fabricated at higher sonication time. From the EDS analysis, the different sites in the nanocomposites’ microstructure were identified which were then correlated with the observation made in the fractographic analysis.