For radiotherapy treatment, scanned proton therapy is a highly conformal treatment technique and can provide increased healthy tissue sparing compared to photons or scattered protons. However, due to the time structure of the scanned beams this technique is highly sensitive to uncertainties and needs to be monitored when treating moving tumours. One example is lung cancer with tumours that move during breathing. In this thesis we looked into the necessity of daily or weekly motion monitoring for moving targets. Furthermore, breath-holding to limit the motion has been investigated for scanned proton treatments. We have also applied a good quality 4D-imaging technique to monitor the motion on a daily basis. At last, we investigated for esophageal tumours a method to correct for changes in motion on a daily basis. The work presented in this thesis will help improve treatment of moving targets with proton therapy.