A synthesized formulation of classical, neoclassical and anomalous transport in toroidal confinement systems with electromagnetic fluctuations and large mean flows is presented. The positive-definite entropy production rate and the conjugate flux–force pairs are rigorously defined for each transport process. The Onsager symmetries of the classical and neoclassical transport matrices are derived from the self-adjointness of the linearized collision operator. The linear gyrokinetic equation with given electromagnetic fluctuations determines the anomalous fluxes with the quasilinear anomalous transport matrix, which satisfies the Onsager symmetry.