On Mars, Laser-Induced Breakdown Spectroscopy (LIBS) as performed by the ChemCam instrument can be used to measure the hydrogen content of targets in situ, under a low pressure CO2 atmosphere. However, unexpected variations observed in the Martian dataset suggest an effect related to target roughness. Here, we present a series of laboratory experiments that reproduce the effect observed on Mars and explore possible causes. We show that the hydrogen peak intensity increases significantly with increasing exposure of the target surface to the LIBS plasma, and that these variations are specific to hydrogen, as other emission lines in the spectra are not affected. The increase of the signal could be related to an addition of hydrogen to the plasma due to interaction with the surrounding target surface, yet the exact physical process to explain such effect remains to be identified. More generally, this effect should be taken into account for the quantification of hydrogen in any LIBS applications where the roughness of the target is significant. Display omitted •The LIBS hydrogen signal specifically varies near protrusions or cavities in Mars targets.•Experiments confirm variations of the LIBS hydrogen signal due to millimeter-scale surface roughness.•Careful target selection is necessary for the quantification of hydrogen by LIBS on Mars.