This paper presents a numerical simulation of the magnetohydrodynamic (MHD) liquid metal flow around a square cylinder placed in a rectangular duct. In the hydrodynamic case, for a certain parameter range the well-known Kármán vortex street with three-dimensional flow patterns is observed, similar to the flow around a circular cylinder. In this study a uniform magnetic field aligned with the cylinder is applied and its influence on the formation and downstream transport of vortices is investigated. The relevant key parameters for the MHD flow are the Hartmann number M, the interaction parameter N and the hydrodynamic Reynolds number, all based on the side length of the cylinder. The Hartmann number M was varied in the range 0 [les ] M [les ] 85 and the interaction parameter N in the range 0 [les ] N [les ] 36. Results are presented for two fixed Reynolds numbers Re = 200 and Re = 250. The magnetic Reynolds number is assumed to be very small. The results of the numerical simulation are compared with known experimental and theoretical results. The hydrodynamic simulation shows characteristic intermittent pulsations of the drag and lift force on the cylinder. At Re = 200 a mix of secondary spanwise three-dimensional instabilities (A and B mode, rib vortices) could be observed. The spanwise wavelength of the rib vortices was found to be about 2–3 cylinder side lengths in the near wake. At Re = 250 the flow appears more organized showing a regular B mode pattern and a spanwise wavelength of about 1 cylinder side length. With an applied magnetic field a quasi-two-dimensional flow can be obtained at low N ≈ 1 due to the strong non-isotropic character of the electromagnetic forces. The remaining vortices have their axes aligned with the magnetic field. With increasing magnetic fields these vortices are further damped due to Hartmann braking. The result that the ‘quasi-two-dimensional’ vortices have a curvature in the direction of the magnetic field can be explained by means of an asymptotic analysis of the governing equations. With very high magnetic fields the time-dependent vortex shedding can be almost completely suppressed. By three-dimensional visualization it was possible to show characteristic paths of the electric current for this kind of flow, explaining the action of the Lorentz forces.