Hydrogen-based energy systems appear to be an attractive proposition in providing a future replacement for the current fossil-fuel based energy systems. Hydrogen is an important, though little studied, trace component of the atmosphere. It is present at the mixing ratio of about 510 ppb currently and has important man-made and natural sources. Because hydrogen reacts with tropospheric hydroxyl radicals, emissions of hydrogen to the atmosphere perturb the distributions of methane and ozone, the second and third most important greenhouse gases after carbon dioxide. Hydrogen is therefore an indirect greenhouse gas with a global warming potential GWP of 5.8 over a 100-year time horizon. A future hydrogen economy would therefore have greenhouse consequences and would not be free from climate perturbations. If a global hydrogen economy replaced the current fossil fuel-based energy system and exhibited a leakage rate of 1%, then it would produce a climate impact of 0.6% of the current fossil fuel based system. Careful attention must be given to reduce to a minimum the leakage of hydrogen from the synthesis, storage and use of hydrogen in a future global hydrogen economy if the full climate benefits are to be realised.