The compatibility of polydimethylsiloxane (PDMS) channels with certain solvents is a well known problem of soft lithography techniques, in particular when it leads to the swelling of the PDMS blocks. However, little is known about the modification of microchannel geometries when they are subjected to swelling solvents. Here, we experimentally measure the deformations of the roof of PDMS microchannels due to such solvents. The dynamics of impregnation of the solvents in PDMS and its relation to volume dilation are first addressed in a model experiment, allowing the precise measurement of the diffusion coefficients of oils in PDMS. When Hexadecane, a swelling solvent, fills a microchannel 1 mm in width and 50 μm in height, we measure that the channel roof bends inwards and takes a parabolic shape with a maximum deformation of 7 μm. The amplitude of the subsidence is found to increase with the channel width, reaching 28 μm for a 2 mm wide test section. On the other hand, perfluorinated oils do not swell the PDMS and the microchannel geometry is not affected by the presence of perfluorodecalin. Finally, we observe that the trajectories of droplets flowing in this microchannel are strongly affected by the deformations: drops carried by swelling oils are pushed towards the edges of the channel while those carried by non-swelling oils remain in the channel center.