We perform a linear stability analysis of three-layer radial porous media and Hele-Shaw flows with variable viscosity in the middle layer. A nonlinear change of variables results in an eigenvalue problem that has time-dependent coefficients and eigenvalue-dependent boundary conditions. We study this eigenvalue problem and find upper bounds on the spectrum. We also give a characterization of the eigenvalues and prescribe a measure for which the eigenfunctions are complete in the corresponding L 2 space. The limit as the viscous gradient goes to zero is compared with previous results on multi-layer radial flows. We then numerically compute the eigenvalues and obtain, among other results, optimal profiles within certain classes of functions.