Two methods of flow measurement in stacks are investigated to determine their errors in presence of cyclonic flow. One method – based on velocity measurements with a Pitot tube in a grid of points – is the standard reference method according to EN ISO 16911-1. The second method – ultrasonic flow measurement – is often used as the automated measurement system in stacks according to EN ISO 16911-2. Several typical stack configurations are considered and the flow field in the stacks is obtained using validated computational fluid dynamics (CFD) modelling with OpenFoam software. We show that possible errors of the standard reference method due to the cyclonic flow are significant compared to the requirements of the EU's Emissions Trading System. For the ultrasonic flow meter we compare various configurations (number, orientation, position) of the ultrasound beams and we demonstrate the flow profile pre-investigation by CFD as prescribed in section 8.3 of EN ISO 16911-2.