This paper documents a novel fast method, named the Iterative Minimum Zone Algorithm (IMZA), for the evaluation of cylindricity deviation on a large number of measurement points, which plays a crucial role in the quality control of high-value products and components when a measurement is undertaken by a modern instrument, such as roundness tester, 3D laser/CT scanner. Firstly, the cylindricity deviation model and the minimum zone’s theoretical basis are presented. Secondly, the Six-point-subset (SPS) and the replacement strategy are introduced, together with the detailed algorithm. The method strictly adheres to the latest ISO definition. A comparison between the proposed method and the typical approaches is carried out on both simulated data and measured data. The results show that IMZA can fast and accurately evaluate the cylindricity deviation with a large number of measurement points.