We investigated the role of lithospheric folding in the Quaternary inversion of the Pannonian basin by a series of analogue models. To this aim, build-up of stresses due to intraplate compression in the hot and weak Pannonian lithosphere, changes in the style of deformation and related surface processes were modelled. The primary response of the lithosphere to compression appears to be deformation in the form of large-scale folding. As a consequence of the folding, differential crustal motions occur, affecting present-day surface morphology and landscape processes. The analogue experiments examined folding mechanisms of the hot Pannonian lithosphere characterised by extremely low strengths except for a thin layer of brittle upper crust. Modelling results confirmed the existence of a large wavelength (∼ 350-400 km) component of deformation accounting for large-scale vertical crustal motions. The amplitude of folding is sufficient to generate the amount of observed uplift and subsidence. Our analogue models, supported by the results of stress analyses, suggest that despite the low rate of convergence between the Adriatic microplate ("Adria-push") and the European plate, the weak Pannonian lithosphere has been an efficient transmitter of compression during the basin inversion. Crustal thickness variations are of key importance in governing regional deformation pattern and influence the timing and extent of the basin inversion. Effects of alternating strong and weak units in the brittle crust were also examined by means of two series of conceptual models, in which the order of thin and thick crustal blocks was opposite. Strain localisation in the brittle crust was strongly controlled by the moderate initial thickness variations. The concept gives a plausible explanation for the presence of anomalous rates of uplift and subsidence and multi-wavelength folding inside the basin. Models taking into account horizontal movements due to lateral extrusion were constructed with an oblique face of the indenter. This kinematic boundary condition resulted in a complex internal structure of the folded layers. The presented analogue experiments, together with previous numerical modelling studies, demonstrate the link between large-scale lithospheric folding and topography evolution in the Pannonian basin system. © 2009 Elsevier B.V. All rights reserved.