Osseointegration of dental implants occurs on a hierarchy of length scales down to the atomic level. A deeper understanding of the complex processes that take place at the surface of an implant on the smallest scale is of interest for the development of improved biomaterials. To date, transmission electron microscopy (TEM) has been utilized for examination of the bone-implant interface, providing details on the nanometer level. In this study we show that TEM imaging can be complemented with atom probe tomography (APT) to reveal the chemical composition of a Ti-based dental implant in a human jaw on the atomic level of resolution. As the atom probe technique has equal sensitivity for all elements, it allows for 3 dimensional characterizations of osseointegrated interfaces with unprecedented resolution. The APT reconstructions reveal a Ca-enriched zone in the immediate vicinity of the implant surface. A surface oxide of some 5nm thickness was measured on the titanium implant, with a sub-stoichiometric composition with respect to TiO2. Minor incorporation of Ca into the thin oxide film was also evident. We conclude that the APT technique is capable of revealing chemical information from the bone-implant interface in 3D with unprecedented resolution, thus providing important insights into the mechanisms behind osseointegration. Osseointegration of dental implants occurs on a hierarchy of length scales down to the atomic level. A deeper understanding of the complex processes that take place at the surface of an implant on the smallest scale is of interest for the development of improved biomaterials. To date, transmission electron microscopy (TEM) has been utilized for examination of the bone-implant interface, providing details on the nanometer level. In this study we show that TEM imaging can be complemented with atom probe tomography (APT) to reveal the chemical composition of a Ti-based dental implant in a human jaw on the atomic level of resolution. Correlative microscopy ensures the accuracy of APT reconstructions and helps provide both chemical and structural information of the bone-implant interface on the smallest of length scales.