The majority of human kidney stones are composed of multiple calcium oxalate crystals with variable amounts of brushite [dicalcium phosphate dihydrate (DCPD)] and hydroxyapatite (HAP) as a nucleus, in which fluid-mediated dissolution and reprecipitation may result in the phase transformation of DCPD to HAP. However, the underlying mechanisms of the phase transition and its modulation by natural inhibitors, such as osteopontin (OPN) proteins, remain poorly understood. Here, the in vitro formation of new phases on the DCPD (010) surface is observed in situ using atomic force microscopy in a simulated hypercalciuria milieu. We demonstrate the presence of an acidic amorphous calcium phosphate (ACP) phase with a characteristic Raman band of nu 1HPO42- and the octacalcium phosphate (OCP)-like phase during the transformation process. High-resolution transmission electron microscopy analyses also confirm the existence of OCP and HAP within an amorphous matrix phase. In support of clinical observations, we further demonstrate the inhibitory effect of OPN peptide segments on the dissolution of DCPD and reprecipitation of acidic ACP. The definition of respective roles of DCPD and OPN thereby provides insights into the control of nucleus formation and subsequent inhibition of pathological mineralization.