Inherent variation of the measurement system, part-to-part variation and variation arising due to the operator are considered to be the most common sources of variation in a measurement system analysis (MSA). Often errors due to within part variation are overlooked, or even worse, are assumed to be from the inherent variation of the measurement system. Understanding the sources of variation in a measurement system is important for all measurement applications. It becomes even more critical when the part used to evaluate a gage has a significant within part variation. This is an important source of measurement system error that the current procedures followed for MSA studies do not clearly or adequately address. The primary reason for this is a lack of awareness, and there are no clear guidelines on conducting a MSA study under these circumstances. A detailed analysis of the effects of within part variation on MSA is described in this paper. An improved method for conducting the MSA under these circumstances is also presented. This improved and more effective MSA takes all sources of variations into consideration.