Several recent studies have shown that fluorescent particles can be localized with an accuracy that is well beyond traditional resolution limits. Using a theoretical model of the image formation process that accounts for possible sources of noise, Cram´er-Rao bounds have been used to define the theoretical limits. A crucial influence on these bounds is the mismatch of refractive indices that is usually present between immersion medium and specimen. This results in an axially shift-variant point spread function, meaning that the bounds change as a function of the particle’s position in the zdirection. We investigate the theoretical bounds for this shiftvariant model, and propose a maximum-likelihood estimator for the particle position in 3D (XYZ position). Using this estimator, sub-resolution localization at the nanometer scale is demonstrated on experimental data. The results provide optimal conditions for particle tracking and localization experiments.