An "almost diagonal" reduced density matrix (in coordinate representation) is usually a result of environment induced decoherence and is considered the sign of classical behavior. We point out that the proton of a ground state hydrogen atom can possess such a density matrix. We demonstrate on this example that an "almost diagonal" reduced density matrix may derive from an interaction with a low number of degrees of freedom (in our case with a single electron) which play the role of the environment. We also show that decoherence effects in our example can only be observed if the interaction with the measuring device is significantly faster than the interaction with the environment (the electron). In the opposite case, when the interaction with the environment is significant during the measurement process, coherence is restored. Finally, we propose a neutron scattering experiment on cold He atoms to observe decoherence which shows up as an additional contribution to the differential scattering cross section.