The GSI carbon ion radiotherapy facility established the first completely active beam shaping system for heavy ions, using energy variation on the synchrotron and pencil beam scanning. The introduction of an active beam shaping system for carbon ions has considerable impact on the design of the treatment planning system (TPS). The TPS has to account for the capability of the beam delivery and the biological modelling, which is needed to calculate the RBE for the resulting varying depth dose modulation. The TPS used in clinical routine with carbon ions is described and its use in treatment planning studies are outlined. A clinical trial with carbon ion therapy as primary therapy for chordoma and chondrosarcoma of the base of skull has been completed in 2001. Currently, carbon ion therapy as a boost treatment together with conventional conformal photon therapy or IMRT is under investigation in clinical trials for adenoid cystic carcinoma, chordoma and chondrosarcoma of the cervical spine and sacrococcygeal chordoma. Treatment planning studies comparing carbon ion therapy with IMRT, using optimization of combination therapy, and optimization of beam-line design have already been completed. Analysis of uncertainties in treatment planning has been started with the investigation of range uncertainties stemming from CT imaging. Uncertainties coming from the beam delivery play only a minor role. An attempt to asses the uncertainties introduced in treatment plans by the biological modelling, was done, using phantom verification of calculated cell survival levels. The clinical trials and planning studies are of special importance for the upcoming new clinical ion facility of the Heidelberg university hospital.