Laterally aligned SnO2 nanowires, which exhibit planar growth along crystallographically defined directions of a sapphire substrate surface, are superior for bio- and gas-sensing applications. Little is known about their cross-sectional geometry and the defect distribution within the nanowire cross section, although this substantially determines the electronic properties of the nanowires. In this study, SnO2 nanowires were grown on r-plane sapphire substrates. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) reveal the highly oriented growth of the SnO2 nanowires toward the substrate edges. High-resolution transmission electron microscopy (HRTEM) of the NW cross section and strain mapping allowed for analyzing the crystallographic alignment of the SnO2 NW to the sapphire substrate and the defect distribution within the SnO2 nanowire cross section. These techniques revealed a defect-free SnO2–Al2O3 interface and a high alignment of the SnO2 NW lattice toward the sapphire substrate along the NW width. The determined high defect density close to the nanowire surface will be discussed in comparison to freestanding SnO2 nanowires and SnO2 thin films on sapphire substrates considering the differences in the growth direction and the interface dimensionality.