For intermediate and high risk prostate cancer, both the prostate gland and seminal vesicles are included in the clinical target volume. Internal motion patterns of these two organs vary, presenting a challenge for adaptive treatment. Adaptive techniques such as isocenter repositioning and soft tissue alignment are effective when tumor volumes only exhibit translational shift, while direct re-optimization of the intensity-modulated radiation therapy (IMRT) plan maybe more desirable when extreme deformation or differential positioning changes of the organs occur. Currently, direct re-optimization of the IMRT plan using beamlet (or fluence map) has not been reported. In this study, we report a novel on-line re-optimization technique that can accomplish plan adjustment on-line. Deformable image registration is used to provide position variation information on each voxel along the three dimensions. The original planned dose distribution is used as the 'goal' dose distribution for adaptation and to ensure planning quality. Fluence maps are re-optimized via linear programming, and a plan solution can be achieved within 2 min. The feasibility of this technique is demonstrated with a clinical case with large deformation. Such on-line ART process can be highly valuable with hypo-fractionated prostate IMRT treatment.