The helix is a complex geometrical element. During the process of a dynamical measurement of the helical deviations, many factors, including the machine and the environment, lead to measurement errors. Although ISO as well as national standards stipulate the tolerances and assessment methods for helical deviations, these standards contribute little to the uncertainty calculations concerning such measurements. According to the Guide to the Expression of Uncertainty in Measurement (GUM), all measurement results must have a stated uncertainty associated to them. But in most cases of helical deviation measurements, no uncertainty value is given, simply because no measurement uncertainty calculation procedure exists. For the case of helical deviation measurements on a Computer Numeric Control (CNC) polar coordinate machine, this paper analyses in detail all kinds of factors contributing to the measurement uncertainty, and gives the calculation procedure of the measurement uncertainty of helical deviation. As an example, the calculation of the measurement uncertainty of the helical deviations of a worm is presented.