A discussion regarding the alignment and measuring procedure of propeller shafts has arose due to the competing situation in the industry, and higher standards from the customers. An estimation of the deflection of shafts in different alignment situations has been made with help of FEM-analysis and beam theory. This has been analyzed and compared with the experience from Rolls-Royce AB suppliers of shafts. An evaluation of measuring protocols has been made and the result indicates that there is a correlation between the deflection of the shaft and the run out. Results from a measuring test performed by Balino, Spain, verifies this conclusion.