The bulk of the Galactic Cosmic Rays (with energies up to 1015 eV) is believed to be accelerated in the shock fronts of supernova remnants. Current Imaging Air Cherenkov Telescopes like H.E.S.S. with their high sensitivity and very good angular resolution are perfect instruments for the observation of these objects in Very High Energy (several 100 GeV up to 100 TeV) gamma-rays, radiation which is produced in the interactions of accelerated protons with ambient material. On this poster we will focus on the case of shell-type supernova remnants associated with molecular clouds. The presence of dense molecular clouds provides substantial target for high energy particles and can be thus used to probe the presence of accelerated hadrons. Several associations traced by 1720 MHz OH masers have been detected by H.E.S.S. and the VHE gamma-ray emission correlates with the matter distribution. High energy gamma-ray have been also detected by Fermi toward these associations. We will discuss the origin of the gamma-ray in terms of cosmic-rays acceleration within the remnants. We will as well estimate the detection potential by neutrino instruments. Traditionnal supernova remnants detected with H.E.S.S. are presented on a separate poster.