Molecular clouds interact with the ambient cosmic rays. The decay of secondary particles may give rise to a detectable flux of very high-energy photons. Recently the H.E.S.S., MAGIC and VERITAS telescopes have observed such sources associated with large molecular clouds and shell-type supernova remnants. Emission lines of OH masers are also observed in coincidence. This ensures that the expanding wave front of the supernova interacts effectively with the cloud. Such natural configurations bring new material to confront with the hypothesis that supernova remnants are the Galactic cosmic-ray accelerators. We describe the approach towards a systematic observation of such associations, present the current data and review the prospects of these studies for answering the question of the origin of the Galactic cosmic rays.