We study the X-ray properties of 39 AGN (24 radio-quiet [RQ] and 15 radio-loud [RL]) with double-peaked Balmer emission lines. 28 of them are Sloan Digital Sky Survey (SDSS) AGN serendipitously observed with ROSAT, XMM-Newton, or Chandra; an additional 11 previously studied double-peaked RL AGN are considered for comparison purposes. Double-peaked Balmer lines originate in the accretion disk and are an important diagnostic of the accretion flow. We find that the ratio of UV-to-X-ray emission, α ox, of RQ double-peaked AGN are similar to those of normal RQ AGN with comparable UV luminosities. Most RL double-peaked AGN are more X-ray luminous than normal RQ AGN, as expected for RL objects. For both RL and RQ double-peaked AGN a few notable exceptions appear X-ray underluminous for their UV luminosity. The spectral shapes of double-peaked AGN are also consistent with those of other objects with similar radio properties.