Weakly nonlinear descriptions of axisymmetric cnoidal and solitary waves in vortices recently have been shown to have strongly nonlinear counterparts. The linear stability of these strongly nonlinear waves to three-dimensional perturbations is studied, motivated by the problem of vortex breakdown in open flows. The basic axisymmetric flow varies both radially and axially, and the linear stability problem is therefore nonseparable. To regularize the generalization of a critical layer, viscosity is introduced in the perturbation problem. In the absence of the waves, the vortex flows are linearly stable. As the amplitude of a wave constituting the basic flow increases owing to variation in the level of swirl, stability is first lost to non-axisymmetric ‘bending’ modes. This instability occurs when the wave amplitude exceeds a critical value, provided that the Reynolds number is larger enough. The critical wave amplitudes for instability typically are large, but not large enough to create regions of closed streamlines. Examination of the most-amplified eigenvectors shows that the perturbations tend to be concentrated downstream of the maximum streamline displacement in the wave, in a position consistent with the observed three-dimensional perturbations in the interior of a bubble type of vortex breakdown.