The Greater Geneva Basin is one of the key targets for geothermal exploration in Switzerland. Until recently, information about the subsurface structure of this region was mostly composed of well-logs, seismic reflection lines, and gravity measurements. As part of the current effort to further reduce subsurface uncertainty, and to test passive seismic methods for exploration purposes, we performed an ambient-noise tomography of the Greater Geneva Basin. We used ∼1.5 years of continuous data collected on a temporary seismic network composed of 28 broadband stations deployed within and around the basin. From the vertical component of the continuous noise recordings, we computed cross-correlation functions and retrieved Rayleigh-wave group-velocity dispersion curves. We then inverted the dispersion curves to obtain 2D group-velocity maps and proceeded to a subsequent inversion step to retrieve a large-scale 3D shear-wave velocity model of the basin. We discuss the retrieved features of the basin in the light of local geology, previously acquired geophysical datasets, and ongoing geothermal exploration. The Greater Geneva Basin is an ideal natural laboratory to test innovative geothermal exploration methods because of the substantial geophysical datasets available for comparison. While we point out the limits of ambient-noise exploration with sparse networks and current methodology, we also discuss possible ways to develop ambient-noise tomography as an affordable and efficient subsurface exploration method.