With the growing use and complexity of proton therapy, the safety and accuracy of the machines becomes increasing important. This, to be able to deliver the prescribed dose to the target while minimizing the dose to healthy tissue. In this project, machine quality assurance data are analyzed to quantify the existing positional machine uncertainties in the form of deviations from expected value and their effect on the dose accuracy in order to improve precision. The method consisted of two main parts. In the first part, two systems to monitor the measured deviations variations from the machine quality assurance tests were implemented. In the second part, two ways to measure the impact of the positional machine uncertainties were developed. The monitoring systems showed that the uncertainties had shrunken over time or were stable, and that the tolerance limits currently used for the machine quality assurance can be lowered. The measured impact of the positional machine uncertainties showed that a margin of 0.61 mm for treatment room 1 and a margin of 1.02 mm for treatment room 2 was required to compensated for the machine uncertainties. When the uncertainties we reincorporated into a clinical approved robust optimized plan, the result showed no significant change in dose to the different treatment volumes. The result gives the Scandion clinic insight and tools to minimize the impact of machine uncertainties and to be able to improve the precision of future treatments.