Over the past decade, strong interactions of light and matter at the single-photon level have enabled a wide set of scientific advances in quantum optics and quantum information science. This work has been performed principally within the setting of cavity quantum electrodynamics with diverse physical systems, including single atoms in Fabry-Perot resonators, quantum dots coupled to micropillars and photonic bandgap cavities and Cooper pairs interacting with superconducting resonators. Experiments with single, localized atoms have been at the forefront of these advances with the use of optical resonators in high-finesse Fabry-Perot configurations. As a result of the extreme technical challenges involved in further improving the multilayer dielectric mirror coatings of these resonators and in scaling to large numbers of devices, there has been increased interest in the development of alternative microcavity systems. Here we show strong coupling between individual caesium atoms and the fields of a high-quality toroidal microresonator. From observations of transit events for single atoms falling through the resonator's evanescent field, we determine the coherent coupling rate for interactions near the surface of the resonator. We develop a theoretical model to quantify our observations, demonstrating that strong coupling is achieved, with the rate of coherent coupling exceeding the dissipative rates of the atom and the cavity. Our work opens the way for investigations of optical processes with single atoms and photons in lithographically fabricated microresonators. Applications include the implementation of quantum networks, scalable quantum logic with photons, and quantum information processing on atom chips.