Transmission spectroscopy to date has detected atomic and molecular absorption in Jupiter-sized exoplanets, but intense efforts to measure molecular absorption in the atmospheres of smaller (Neptune-sized) planets during transits have revealed only featureless spectra. From this it was concluded that the majority of small, warm planets evolve to sustain high mean molecular weights, opaque clouds, or scattering hazes in their atmospheres, obscuring our ability to observe the composition of these atmospheres. Here we report observations of the transmission spectrum of HAT-P-11b (~4 Earth radii) from the optical to the infrared. We detected water vapour absorption at 1.4 micrometre wavelength. The amplitude of the water absorption (approximately 250 parts-per- million) indicates that the planetary atmosphere is predominantly clear down to ~1 mbar, and sufficiently hydrogen-rich to exhibit a large scale height. The spectrum is indicative of a planetary atmosphere with an upper limit of ~700 times the abundance of heavy elements relative to solar. This is in good agreement with the core accretion theory of planet formation, in which gas giant planets acquire their atmospheres by directly accreting hydrogen-rich gas from the protoplanetary nebulae onto a large rocky or icy core.
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