Well aligned densely packed IrO₂ nanocrystals (NCs) have been grown on sapphire (SA) substrates with different orientations by reactive magnetron sputtering using an Ir metal target. The surface morphology, structural and spectroscopic properties of the as-deposited NCs were characterized using field-emission scanning electron microscopy (FESEM), x-ray diffraction (XRD), x-ray photoelectron spectroscopy (XPS) and micro-Raman spectroscopy. FESEM micrographs reveal that NCs with parallel in-plane alignment were gown on SA(001), vertically aligned NCs were grown on SA(100), while the NCs on SA(012) and SA(110) contained, respectively, single- and double-aligned directions with a tilt angle of ~35° from the normal to the substrates. The XRD results indicate that the NCs are (100), (001), and (101) oriented on SA(001), SA(001), and SA(012)/SA(110) substrates, respectively. A strong substrate effect on the alignment of the IrO₂ NCs growth has been demonstrated and the probable mechanism for the formation of these NCs has been discussed. XPS analyses show the coexistence of higher oxidation states of iridium in the as-grown IrO₂ NCs. The Raman spectra show the red-shift and asymmetric peak broadening with a low frequency tail of the IrO₂ signatures with respect to that of the bulk counterpart, which are attributed to both the size and residual stress effects.