Measurements of the instantaneous in-cylinder flow fields were carried out in a water analog engine simulation rig using 3-D Particle Tracking Velocimetry. Two different configurations based on a 4-valve per cylinder engine with a typical pent-roof type combustion chamber were investigated. Measurements were performed at the end of intake stroke at BDC for simulated idle conditions. Efforts were made to maximize the particle seeding density (and the resulting number of 3-D velocity vectors) to yield 250 to 300 instantaneous vectors at each cycle. Using an appropriately designed spatial filter the low pass filtered (large scale) instantaneous velocity fields were reconstructed for each cycle. The spatial cut-off of the filter was set to 1/3 of the engine bore diameter. Based on these cycle-resolved flow fields, the cycle-to-cycle variations as well as the cycle resolved turbulence fluctuations were computed.This paper describes the technique used and demonstrates the potential of the 3-D PTV in conjunction with the Water Analog Simulation approach to routinely measure the cycle-to-cycle stability of the ensemble average 3-D dominant flow patterns. This routine measurement is required to develop a flow stability metric that can link engine geometry in-cylinder motion, and combustion repeatability. Such a link will help identify and set design targets for the type of favorable in-cylinder motion that can yield good engine idle stability and reduced emissions.