This paper is part of the special publication No.156, The Mediterranean basins: Tertiary extension within the Alpine Orogen. (eds B.Durand, L. Jolivet, F.Horvath and M.Seranne). Detailed sedimentological, facies and numerical cycle analysis, combined with magnetostratigraphy, have been made in a number of boreholes in the Pannonian Basin, in order to study the causes of relative water-level changes and the history of the basin subsidence. Subsidence and infilling of the Pannonian Basin, which was an isolated lake at that time occurred mainly during the Late Miocene and Pliocene. The subsidence history was remarkably different in the individual sub-basins: early thermal subsidence was interrupted in the southern part of the basin, while high sedimentation rate and continuous subsidence was detected in the northeastern sub-basin. Three regional unconformities were detected in the Late Neogene Pannonian Basin fill, which represent 0.5 and 7.5 Ma time spans corresponding to single and composite unconformities. Consequently two main sequences build up the Late Neogene Pannonian Basin fill: a Late Miocene and a Pliocene one. Within the Late Miocene sequence there are smaller sedimentary cycles most probably corresponding to climatically driven relative lake-level changes in the Milankovitch frequency band. Considering the periods, the estimated values for precession and eccentricity in this study (19 and 370 ka) are close to the usually cited ones. In the case of obliquity the calculated period (71 ka) slightly deviates from the generally accepted number. Based on the relative amplitudes of oscillations, precession (sixth order) and obliquity (fifth order) cycles had the most significant impact on the sedimentation. Eccentricity caused cycles (fourth order) are poorly detectable in the sediments. The longer term (third order) cycles had very slight influence on the sedimentation pattern. Progradation, recorded in the Late Miocene sequence, correlates poorly in time within the basin. The dominant controls of this process probably were changes of basin subsidence rate and the very high sedimentation rate. The slow, upward trend of silt and sand bed thickness as well as that of the grain size also reflects the local progradation.