The stability of circular vortices to normal mode perturbations is studied in a multi-layer quasi-geostrophic model. The stratification is fitted on the Gulf of Cadiz where many Mediterranean Water (MW) eddies are generated. Observations of MW eddies are used to determine the parameters of the reference experiment; sensitivity tests are conducted around this basic case. The objective of the study is two-fold: (a) determine the growth rates and nonlinear evolutions of unstable perturbations for different three-dimensional (3D) velocity structures of the vortices, (b) check if the different structure of our idealized vortices, mimicking MW cyclones and anticyclones, can induce different stability properties in a model that conserves parity symmetry, and apply these results to observed MW eddies. The linear stability analysis reveals that, among many 3D distributions of velocity, the observed eddies are close to maximal stability, with instability time scales longer than 100 days (these time scales would be less than 10 days for vertically more sheared eddies). The elliptical deformation is most unstable for realistic eddies (the antisymmetric one dominates for small eddies and the triangular one for large eddies); the antisymmetric mode is stronger for cyclones than for anticyclones. Nonlinear evolutions of eddies with radii of about 30 km, and elliptically perturbed, lead to their re-organization into 3D tripoles; smaller eddies are stable and larger eddies break into 3D dipoles. Horizontally more sheared eddies are more unstable and sustain more asymmetric instabilities. In summary, few differences were found between cyclone and anticyclone stability, except for strong horizontal velocity shears.