All measurements include uncertain factors affecting the result in accordance with environment and conditions. In order to guarantee right decision making and quality improvement, these factors must be found and appropriate actions should be taken. This paper aims to estimate and analyze variabilities found in set-up and as well as measurement uncertainty when using CMM(Coordinate Measuring Machine). Two skilled operators were selected to individually measure a product which was a kind of main part of an engine called connecting rod cap. The results showed that at the least, 10 % was stable while at the most, 30 % was somewhat unstable regarding P, percentage of measuring errors. There was little difference between the two operators on measurement uncertainty expecially considering their degree of freedom based on their objective and subjective judgement of type B uncertainty despite the significant difference between them. Through this research, I have come to a conclusion that a much more detailed analysis on variation factors can be identified in general measurement by using CMM and the result of set-up variability demands specific investigation and efforts to improve operators’ skill or thorough examination on the method of setting product to minimize set-up variability later.