The three-dimensional, compressible Navier–Stokes equations in primitive variables are solved numerically to simulate vortex breakdown in a constricted tube. Time integration is performed with an implicit Beam-Warming algorithm using fourth-order compact operators to discretize spatial derivatives. Initial conditions are obtained by solving the steady, compressible, and axisymmetric form of the Navier–Stokes equations with Newton’s method. The effects of three-dimensionality on flows that are initially axisymmetric and stable to 2-D disturbances are examined. Stability of the axisymmetric base flow is assessed through 3-D time integration. Axisymmetric solutions at a Mach number of 0.3 and a Reynolds number of 1000 contain a region of nonuniqueness. Within this region, 3-D time integration reveals only unique solutions, with nonunique axisymmetric initial conditions converging to a unique solution that is steady and axisymmetric. Past the primary limit point, which approximately identifies the appearance of critical flow (a flow that can support an axisymmetric standing wave), the solutions bifurcate into 3-D time-periodic flows. Thus this numerical study shows that the vortex strength associated with the loss of stability to 3-D disturbances and that of the primary limit point are in close proximity. Additional numerical and theoretical studies of 3-D swirling flows are needed to determine the impact of various parameters on dynamic behavior. For example, it is possible that a different flow behavior, leading to a nearly axisymmetric vortex breakdown state, may develop with other inlet profiles and tube geometries.