The incorporation of daily images into the radiotherapy process leads to adaptive radiation therapy (ART), in which the treatment is evaluated periodically and the plan is adaptively modified for the remaining course of radiotherapy. Deformable registration between the planning image and the daily images is a key component of ART. In this paper, we report our researches on deformable registration between the planning kVCT and the daily MVCT image sets. The method is based on a fast intensity-based free-form deformable registration technique. Considering the noise and contrast resolution differences between the kVCT and the MVCT, an 'edge-preserving smoothing' is applied to the MVCT image prior to the deformable registration process. We retrospectively studied daily MVCT images from commercial TomoTherapy machines from different clinical centers. The data set includes five head-neck cases, one pelvis case, two lung cases and one prostate case. Each case has one kVCT image and 20-40 MVCT images. We registered the MVCT images with their corresponding kVCT image. The similarity measures and visual inspections of contour matches by physicians validated this technique. The applications of deformable registration in ART, including 'deformable dose accumulation', 'automatic re-contouring' and 'tumour growth/regression evaluation' throughout the course of radiotherapy are also studied.