We have implemented in the Geant4 simulation toolkit a set of new ionisation cross sections for the simulation of particle induced X-ray emission (PIXE), based upon theoretical and semi-empirical models. The set provides a model based on the so-called ECPSSR theory for the computation of K-shell ionisation cross sections for proton and alpha particle impact. A second model is based upon semi-empirical expressions proposed by Orlic for the calculation of Li-subshells ionisation cross sections for proton impact. Our developments are compared to ionisation cross sections already existing in the Geant4 toolkit and to experimental data.