We report the results of X-ray (2-10 keV) observations of the giant molecular clouds Sgr B, Sgr C and Sgr D in the Galactic Center region, together with the discovery of the point-like source SAX J1748.2-2808. The data have been obtained with the MECS instrument on the BeppoSAX satellite. The core of Sgr B2 has an X-ray luminosity of 6*1034 erg s-1 and its spectrum is characterized by a strong Fe emission line at 6.5 keV with an equivalent width of 2 keV. Faint diffuse X-ray emission is detected from Sgr C and from the SNR G1.05-0.15 (Sgr D). A new, unresolved source with a strong Fe line has been discovered in the Sgr D region. This source, SAX J1748.2-2808, is probably associated with a SiO and OH maser source at the Galactic Center distance. If so, its luminosity is 1034 erg s-1. We propose that the X-ray emission from SAX J1748.2-2808 is produced either by protostars or by a giant molecular cloud core. Emission from sources similar to SAX J1748.2-2808 could have an impact on the expected contribution on the observed Fe line emission from the Galactic ridge.