Objectives: The accuracy of delivered dose depends directly upon initial beam calibration and subsequent maintenance of this beam output. The uncertainty associated with these measurements and its impact on clinical outcomes is not well documented. This work gives an evidence based approach to determining this variation and its clinical impact. Novelty: This work will quantify for the first time the variations present in the routine maintenance of beam output on a national scale. The novel application of these dosimetric uncertainties to radiobiological models is then employed to predict the variation in clinical outcome due to the quantified dosimetric variations for specific clinical cases, including both tumour control and associated treatment complications on both individual and patient populations. Results: The linear-quadratic and Lyman Kutcher Burman models have been implemented to allow flexibility in the modelling of individual patient doses on a fraction by fraction basis. The variation in delivered doses due to beam output variations is seen to be normally distributed with a standard deviation of 0.7%. These variations may lead to a typical patient experiencing a range in treatment outcome probabilities of over 10% for cancers with a steep dose response curve such as head and neck in both the case of an individual patient and for a patient population. Conclusions: The precise control of beam output is shown to be a major factor in the overall uncertainty for dose delivery in modern treatment techniques. With reductions in other uncertainties in radiotherapy treatments, now may be the time to consider reduction of tolerance levels to allow optimal patient treatment and outcomes.