Measurements of the deuterium-to-hydrogen ratios (D/H) in the fields of meteorology1,2, tropospheric3,4 and stratospheric chemistry5,6, planetology7,8 and cosmogony8,9 have previously been performed on molecules in which one hydrogen atom is replaced by one deuterium atom. We report here the first detection of isolated deuterium atoms in the Earth's upper atmosphere through their resonantly scattered Lyman-α emission. An atmospheric deuterium emission of 330 R (1 R=10⁶ photons cm−2 s−1) is observed for a tangent altitude of 110 km during Spacelab 1 mission launched on 28 November 1983. The (D/H) ratio of 3×10−4 is slightly enriched over the seawater value of 1.6×10−4.