Aberration-corrected scanning transmission electron microscopy was used to elucidate the crystalline nature, morphologies and other catalytically relevant properties (such as defect structures and surface stability) of nanoparticulate Ga–Pd selective hydrogenation catalysts. Atomically resolved and chemically sensitive annular dark-field (ADF) imaging revealed, directly, the distinct crystalline structures corresponding to the intermetallic compound GaPd2. A disordered over-layer decorating the surface of the nanoparticles was studied in a spatially resolved manner using ADF imaging and electron energy-loss spectroscopy. The analysis corroborated a partial decomposition of the intermetallic surface and formation of oxidic islands following exposure of the nanoparticles to ambient conditions. The direct imaging of the nanoparticles, the size of which predominantly falls into the sub-10 nm range, revealed their morphologies and significant crystalline defects, including five-fold twinning. The manifestation of the intermetallic compound in the nano-sized catalysts is intriguing from a crystallographic perspective and the observed deviations from the bulk crystal structure are of catalytic significance.