Electron beam irradiation which is considered a reliable method for tailoring the surface charge of hydroxyapatite is hindered by carbon contamination. Separating the effects of the carbon contamination from those of irradiation-induced trapped charge is important for a wide range of biological applications. In this work we focus on the understanding of the electron-beam-induced carbon contamination with special emphasis on the influence of the electron irradiation parameters on this phenomenon. Phase imaging in atomic force microscopy is used to evaluate the influence of electron energy, beam current and irradiation time on the shape and size of the resulted contamination patterns. Different processes involved in the carbon contamination of hydroxyapatite are discussed. (C) 2015 Elsevier B.V. All rights reserved.