Hydraulic instability associated with pressure fluctuations is a serious problem in hydraulic machinery. Pressure fluctuations are usually a result of a strong vortex created in the centre of a flow at the outlet of a runner. At every radial turbine and also at every single regulating axial turbine, the draft tube vortex appears at part-load operating regimes. The consequences of the vortex developed in the draft tube are very unpleasant pressure pulsation, axial and radial forces and torque fluctuation as well as turbine structure vibration. The consequences of the vortex are transferred upstream and downstream with amplitude and frequency modulation in respect of the turbine operating regime, cavitation conditions and air admitted content. Numerical prediction of the vortex appearance in the design stage is a very important task. The amplitude of the pressure pulsation is different for each operating regime therefore the main goal of this research was to numerically predict pressure pulsation amplitude versus different guide vane openings and to compare the results with experimental ones. For the numerical flow analysis of a complete Francis turbine (FT), the computer code ANSYS-CFX11 has been used.