Defect sites on bone minerals play a critical role in bone remodeling processes. We investigated single crystal hydroxyapatite (100) surfaces bearing crystal defects under acidic dissolution conditions using real-time in situ atomic force microscopy. At defect sites, surface structure-dependent asymmetric hexagonal etch pits were formed, which dominated the overall dissolution rate. Meanwhile, dissolution from the flat terraces proceeded by stochastic formation of flat bottom etch pits. The resulting pit shapes were intrinsically dictated by the HAP crystal structure. Computational modeling also predicted different step energies associated with different facets of the asymmetric etch pits. Our microscopic observations of HAP dissolution are significant for understanding the effects of local surface structure on the bone mineral remodeling process and provide useful insights for the design of novel therapies for treating osteoporosis and dental caries.