The recent advances in single atom detection and manipulation in experiments with ultracold quantum gases are reviewed. The discussion starts with the basic principles of trapping, cooling and detecting single ions and atoms. The realization of single atom detection in ultracold quantum gases is presented in detail and the employed methods, which are based on light scattering, electron scattering, field ionization and direct neutral particle detection are discussed. The microscopic coherent manipulation of single atoms in a quantum gas is also covered. Various examples are given in order to highlight the power of these approaches to study many-body quantum systems.