Pre-Main Sequence stars are variable sources. The main mechanisms responsible for their variability are variable extinction, unsteady accretion, and rotational modulation of both hot and dark photospheric spots and X-ray active regions. In stars with disks this variability is thus related to the morphology of the inner circumstellar region (<0.1 AU) and that of photosphere and corona, all impossible to be spatially resolved with present day techniques. This has been the main motivations of the Coordinated Synoptic Investigation of NGC2264, a set of simultaneous observations of NGC2264 with 15 different telescopes. We analyze the X-ray spectral properties of stars with disks extracted during optical bursts and dips in order to unveil the nature of these phenomena. Stars are analyzed in two different samples. In stars with variable extinction a simultaneous increase of optical extinction and X-ray absorption is searched during the optical dips; in stars with accretion bursts we search for soft X-ray emission and increasing X-ray absorption during the bursts. In 9/33 stars with variable extinction we observe simultaneous increase of X-ray absorption and optical extinction. In seven dips it is possible to calculate the NH/AV ratio in order to infer the composition of the obscuring material. In 5/27 stars with optical accretion bursts, we observe soft X-ray emission during the bursts that we associate to the emission of accreting gas. It is not surprising that these properties are not observed in all the stars with dips and bursts since favorable geometric configurations are required. The observed variable absorption during the dips is mainly due to dust-free material in accretion streams. In stars with accretion bursts we observe in average a larger soft X-ray spectral component not observed in non accreting stars. This indicates that this soft X-ray emission arises from the accretion shocks.