Hadrontherapy is a form of radiation therapy, which uses beams of charged particles such as carbon ions. Compared to conventional radiotherapy the main advantage of hadrontherapy is the precise dose-localization along with an increased biological effectiveness. First results obtained from prostate cancer patients treated withhadrontherapy showed good local tumor control and survival rates. We investigated the effects of irradiation with different beam qualities on gene expression changes in the PC3 prostate adenocarcinoma cell line. PC3 cells were irradiated with various doses of carbon ions (LET=33.7 keV/µm) at GANIL (Caen, France). Comparative experiments with X-rays were performed at SCK-CEN. Genome-wide expression was analyzed using microarrays. Our results show downregulation in many genes involved in cell cycle and cell organization after 2.0 Gy irradiation. This effect was more pronounced after carbon ion irradiation compared with X-rays. Furthermore, we found a significant downregulation of many genes related to cell motility. Several of these changes were confirmed using qPCR. In addition, recurrence-free survival analysis of prostate cancer patients based on one of these motility genes (FN1) revealed that patients with low expression levels had a prolonged recurrence-free survival time, indicating that this gene may be a potential prognostic biomarker for prostate cancer.