Aims:X-ray sources at intermediate fluxes (a few × 10-14 erg cm-2 s-1) with a sky density of ~100 deg-2 are responsible for a significant fraction of the cosmic X-ray background at various energies below 10 keV. The aim of this paper is to provide an unbiased and quantitative description of the X-ray source population at these fluxes and in various X-ray energy bands. Methods: We present the XMM-Newton Medium sensitivity Survey (XMS), including a total of 318 X-ray sources found among the serendipitous content of 25 XMM-Newton target fields. The XMS comprises four largely overlapping source samples selected at soft (0.5-2 keV), intermediate (0.5-4.5 keV), hard (2-10 keV) and ultra-hard (4.5-7.5 keV) bands, the first three of them being flux-limited. Results: We report on the optical identification of the XMS samples, complete to 85-95%. At the flux levels sampled by the XMS we find that the X-ray sky is largely dominated by Active Galactic Nuclei. The fraction of stars in soft X-ray selected samples is below 10%, and only a few per cent for hard selected samples. We find that the fraction of optically obscured objects in the AGN population stays constant at around 15-20% for soft and intermediate band selected X-ray sources, over 2 decades of flux. The fraction of obscured objects amongst the AGN population is larger (~35-45%) in the hard or ultra-hard selected samples, and constant across a similarly wide flux range. The distribution in X-ray-to-optical flux ratio is a strong function of the selection band, with a larger fraction of sources with high values in hard selected samples. Sources with X-ray-to-optical flux ratios in excess of 10 are dominated by obscured AGN, but with a significant contribution from unobscured AGN. Based on observations obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA Member States and the USA (NASA). Based on observations made with the INT/WHT, TNG and NOT operated on the island of La Palma by the Isaac Newton Group, the Centro Galileo Galilei and the Nordic Optical Telescope Science Association respectively, in the Spanish Observatorio del Roque de los Muchachos. Based on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC). Based on observations collected at the European Southern Observatory, Paranal, Chile, as part of programme 75.A-0336.