Linear stability of the Stuart vortices in the presence of an axial flow is studied. The local stability equations derived by Lifschitz & Hameiri (Phys. Fluids A, vol. 3 (11), 1991, pp. 2644-2651) are rewritten for a three-component (3C) two-dimensional (2D) base flow represented by a 2D streamfunction and an axial velocity that is a function of the streamfunction. We show that the local perturbations that describe an eigenmode of the flow should have wavevectors that are periodic upon their evolution around helical flow trajectories that are themselves periodic once projected on a plane perpendicular to the axial direction. Integrating the amplitude equations around periodic trajectories for wavevectors that are also periodic, it is found that the elliptic and hyperbolic instabilities, which are present without the axial velocity, disappear beyond a threshold value for the axial velocity strength. Furthermore, a threshold axial velocity strength, above which a new centrifugal instability branch is present, is identified. A heuristic criterion, which reduces to the Leibovich & Stewartson criterion in the limit of an axisymmetric vortex, for centrifugal instability in a non-axisymmetric vortex with an axial flow is then proposed. The new criterion, upon comparison with the numerical solutions of the local stability equations, is shown to describe the onset of centrifugal instability (and the corresponding growth rate) very accurately. © Cambridge University Press 2014.