We report a general framework capable of describing the focusing of electromagnetic waves with spatially varying coherence and polarization properties in optical systems of arbitrary numerical aperture and Fresnel number. We also investigate the reduction of the dimensionality of the requisite integrals by use of a coherent mode expansion. We find that coherent mode expansions treating each component of the electric field vector individually are unsuitable for describing focusing systems because of the inter-component mixing that can occur in high numerical aperture systems. In addition, we show that the assumption of harmonic angular dependence allows the azimuthal integration to be performed analytically, providing further simplification of the analysis. We also find that the effective degree of spectral coherence of an electromagnetic beam is unchanged upon focusing. Finally, as an illustration of the developed framework, we calculate the transverse and axial focal distributions for a partially coherent source formed by incoherent superposition of radially and azimuthally polarized Laguerre-Gauss modes.