Natural gypsum can degenerate into hemihydrate during cement clinker grinding which changes the physical and chemical properties of cement hydration, affecting therefore the fresh and hardened properties of cement based materials. Cement systems containing a constant total amount of calcium sulfate (4%) with relative proportions of hemihydrate and natural gypsum were considered. Rheological measurements were executed on an Anton Paar MCR51 rheometer to evaluate the flow properties of cement pastes. Results show that, the yield stress and the plastic viscosity of cement pastes were affected when the degeneration of natural gypsum exceeded 50%. Above this concentration, the yield stress remarkably increased and a variation in plastic viscosity of about 50% was observed. Using TG-DSC techniques, it was shown that, the amount of formed ettringite could not explain these rheological changes. However, centrifugational packing and SEM-SE measurements confirmed that, more than the amount of ettringite precipitated, ettringite morphology plays a major role in controlling the yield stress and plastic viscosity of fresh cement pastes.