Shales and clay rocks of Neogene age were studied from 38 boreholes in the Pannonian Basin. The effect of geological factors on the transformation of smectite to illite was studied. These factors include the origin of the sedimentary material, facies and postdepositional tectonic evolution. Partial basins and relative structural heights within the Pannonian Basin were considered separately. Terrigeneous clastic rocks deposited in marine or lacustrine environments are the most suitable rock types for the determination of the degree of diagenesis. Clays of in situ or redeposited kaolinitic weathering crusts found at the bottom and in particular horizons within the Neogene sequence usually contain low smectite proportions. Illite/smectites in weathered alluvial and continental clays of the uppermost stratigraphic horizons are of variable composition. On the other hand, smectite proportions in volcanogenic sediments are higher than those in terrigeneous ones in the shallow and transitional zones of diagenesis. In continuously subsiding deep depressions the depth of the transitional zone of diagenesis is in the interval of about 2.0 to 3.5 km. In relatively uplifted areas the transitional zone may start at a depth of several hundred meters and its lower boundary may be found at about 1.5 to 2.0 km subsurface depth. This is due to the erosion of several hundred meters from the upper part of the sedimentary column and to differences in the thermal history of the sequences.