Seyfert's Sextet (a.k.a HCG 79) is one of the most compact and isolated galaxy groups in the local Universe. It shows a prominent diffuse light component that accounts for ~50% of the total observed light. This likely indicates that the group is in an advanced evolutionary phase, which would predict a significant hot gaseous component. Previous X-ray observations had suggested a low luminosity for this system, but with large uncertainties and poor resolution. We present the results from a deep (70 ks), high resolution Chandra observation of Seyfert's Sextet, requested with the aim of separating the X-ray emission associated with the individual galaxies from that of a more extended inter-galactic component. We discuss the spatial and spectral characteristics of this group we derive with those of a few similar systems also studied in the X-ray band. The high resolution X-ray image indicates that the majority of the detected emission does not arise in the compact group but is concentrated towards the NW and corresponds to what appears to be a background galaxy cluster. The emission from the group alone has a total luminosity of ~1x10^40 erg/s in the (0.5-5) keV band. Most of the luminosity can be attributed to the individual sources in the galaxies, and only ~2x10^39 erg/s is due to a gaseous component. However, we find that this component is also mostly associated with the individual galaxies of the Sextet, leaving little or no residual in a truly IGM component. The extremely low luminosity of the diffuse emission in Seyfert's Sextet might be related to its small total mass.