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We present a Chandra X-ray Observatory ACIS-S variability, spectroscopy, andimaging study of the peculiar binary containing the millisecond pulsarJ1023+0038. The X-ray emission from the system exhibits highly significant(12.5 sigma) large-amplitude (factor of 2-3) orbital variability over the fiveconsecutive orbits covered by the observation, with a pronounced decline in theflux at all energies at superior conjunction. This can be naturally explainedby a partial geometric occultation by the secondary star of an X-ray--emittingintrabinary shock, produced by the interaction of outflows from the two stars.The depth and duration of the eclipse imply that the intrabinary shock islocalized near or at the surface of the companion star and close to the innerLagrangian point. The energetics of the shock favor a magnetically dominatedpulsar wind that is focused into the orbital plane, requiring close alignmentof the pulsar spin and orbital angular momentum axes. The X-ray spectrumconsists of a dominant non-thermal component and at least one thermalcomponent, likely originating from the heated pulsar polar caps, although aportion of this emission may be from an optically-thin "corona". We find noevidence for extended emission due to a pulsar wind nebula or bow shock down toa limiting luminosity of L_X<3.6x10^29 ergs s^-1 (0.3-8 keV), <7x10^-6 of thepulsar spin-down luminosity, for a distance of 1.3 kpc and an assumed power-lawspectrum with photon index Gamma=1.5.

A Chandra X-ray Observation of the Binary Millisecond Pulsar PSR J1023+0038