Palaeomagnetic studies were carried out in the Devonian to Early Carboniferous carbonates of the Moravo-Silesian Zone: MSZ (Czech Republic) in order to evaluate the timing and origin of late Variscan magnetic overprinting. Sampling localities were spread out along the strike of the MSZ from the SW to NE. Previously published thermal maturity data have demonstrated a significant gradient from SW (burial temperatures 150 to 200 deg.C) to NE of the region (250 to 300 deg.C). A late Variscan remagnetization direction (component A), carried by magnetite, was identified in 6 localities. Three phases of the remagnetization in the MSZ might be distinguished which might be assigned to Early to Late Carboniferous, Late Carboniferous and Early Permian. They are coeval with remagnetization events distinguished in Ardennes. A correlation exists between thermal indices and unblocking temperature spectra of component A. Thermal activation nomograms show that component A might be either a thermoviscous or thermochemical remanent magnetization acquired due to a thermal event (deep burial) of 1 to 10 My duration and stabilized during subsequent up lift. A more ancient component B, identified in the SW part, previously interpreted as primary, is shown to be a synfolding remagnetisation. It indicates 70 deg. clock wise rotations before the acquisition of the component A.