The halogens (F, Cl, Br and I), H2O and CO2 were investigated in eighteen representative lavas, dykes and a gabbro spanning depths 750–1450 mbsf in the International Ocean Discovery Project (IODP) Hole 1256D. Whole rock analyses of halogens, H2O and CO2, and in situ F and Cl electron microprobe analyses were combined to provide new information about hydrothermal alteration of the ocean crust and the mineral controls on the abundances of all four halogens in altered ocean crust that is subducted into the mantle. Whole rock concentrations of halogens, H2O and CO2 are heterogeneous at all crustal levels with maxima in highly altered zones of fluid infiltration. Nonetheless, Cl and Br show a general increase down the hole from minima of 130 ppm Cl and 330 ppb Br in the lavas, with dominant saponite-chlorite alteration, to maxima of 1620 ppm Cl and 2720 ppb Br in amphibolite facies granoblastic dykes and the gabbros near the base of the hole. In contrast, H2O concentrations of 1.5–2 wt% were common in clay-rich (saponite) alteration with lower values in the deeper amphibole-rich samples. The concentrations of F (130–300 ppm), I (6–25 ppb) and CO2 (0.13–0.43 wt.%) do not show any obvious relationship to depth. The altered lavas, dykes and gabbros are enriched in Cl, Br, I and H2O by ∼2–20 times, but have F concentrations similar to uncontaminated fresh N-MORB glasses from the East Pacific Rise. The majority of amphiboles analysed in this and previous studies have low F/Cl ratios that are typical of hydrothermal amphiboles formed from F-poor seawater-derived fluids. The most Cl-rich amphiboles in the deepest gabbro typically contain ∼2000–4000 ppm Cl, but a patch of amphibole with 1.6 wt.% Cl was found close to a chlorapatite. Together the Cl-rich amphibole and hydrothermal chlorapatite, with up to 5.4 wt.% Cl, provide evidence for high salinity seawater-derived brines (∼50 wt.% salts) at the base of the hole. In addition a population of F-rich amphiboles (>1000 ppm F) with elevated F/Cl ratios (F/Cl ∼ 6–8) provide evidence for the passage of F-rich magmatic fluids in the granoblastic dykes and gabbros. Hydrous silicates including saponite-chlorite at the top of the hole and amphibole below 1300 mbsf, typically accommodate most of the F and Cl (e.g. 20–60%) in whole rock samples. Apatite accommodates a further <5–40% of the total F and Cl, with non-structural sites including grain boundaries and fluid inclusions estimated to accommodate 30–50% of the halogens in many samples. Bromine and I are preferentially hosted by phyllosilicates and non-structural sites, and excluded from amphibole relative to Cl. As a result, saponite-chlorite alteration is characterised by a range of Br/Cl and I/Cl ratios overlapping those typical of the Earth’s mantle, whereas deeper amphibolite facies alteration has lower Br/Cl and I/Cl ratios. Halogen abundance ratios therefore indicate that if subduction of oceanic crust significantly contributes to the halogen inventory of the Earth’s mantle, low-temperature (<150 °C) alteration could be an important reservoir of halogens in the subducting slab.