Traditionally, uncertainties are handled by expanding the irradiated volume to ensure target dose coverage to a certain probability. The uncertainties arise from e.g. the uncertainty in positioning of the patient at every fraction, organ motion and in defining the region of interests on the acquired images. The applied margins are inherently population based and do not exploit the geometry of the individual patient. Probabilistic planning on the other hand incorporates the uncertainties directly into the treatment optimization and therefore has more degrees of freedom to tailor the dose distribution to the individual patient. The aim of this thesis is to create a framework for probabilistic evaluation and optimization based on the concept of dose coverage probabilities. Several computational challenges for this purpose are addressed in this thesis. The accuracy of the fraction by fraction accumulated dose depends directly on the accuracy of the deformable image registration (DIR). Using the simulation framework, we could quantify the requirements on the DIR to 2 mm or less for a 3% uncertainty in the target dose coverage. Probabilistic planning is computationally intensive since many hundred treatments must be simulated for sufficient statistical accuracy in the calculated treatment outcome. A fast dose calculation algorithm was developed based on the perturbation of a pre-calculated dose distribution with the local ratio of the simulated treatment’s fluence and the fluence of the pre-calculated dose. A speedup factor of ~1000 compared to full dose calculation was achieved with near identical dose coverage probabilities for a prostate treatment. For some body sites, such as the cervix dataset in this work, organ motion must be included for realistic treatment simulation. A statistical shape model (SSM) based on principal component analysis (PCA) provided the samples of deformation. Seven eigenmodes from the PCA was sufficient to model the dosimetric impact of the interfraction deformation. A probabilistic optimization method was developed using constructs from risk management of stock portfolios that enabled the dose planner to request a target dose coverage probability. Probabilistic optimization was for the first time applied to dataset from cervical cancer patients where the SSM provided samples of deformation. The average dose coverage probability of all patients in the dataset was within 1% of the requested.