This thesis uses infrared observations from spacecraft and ground-based telescopes to investigate the composition and cloud structure of the jovian atmosphere. It focuses on a single spectral region, known as the 5-μm window, where Jupiter's upper atmosphere becomes optically thin. This allows us to probe down beneath the planet's thick cloud decks to the 4{8 bar region in the middle troposphere. Two different data sources are combined to build up a three-dimensional picture of Jupiter's troposphere. The first dataset is from the Cassini VIMS instrument, and was taken during the 2000-2001 Jupiter yby. These observations cover a wide spectral range, provide global coverage and include both the nightside and the dayside of the planet, making them well suited to studying clouds. The VIMS spectra can be modelled using a single tropospheric cloud deck, subject to the following constraints: (i) the cloud base is located at pressures of 1.2 bar or lower; (ii) the cloud particles are highly scattering; and (iii) the cloud is sufficiently spectrally at. The second dataset is from the CRIRES instrument at the Very Large Telescope in Chile. These observations have a very high spectral resolution, allowing the absorption lines of individual molecular species to be resolved. The CH3D line shape varies between belts and zones, which can be interpreted as variations in the opacity of a deep cloud, located at around 5 bar. There is also evidence for spatial variability in two disequilibrium species, AsH3 and PH3, both of which show an enhancement at high latitudes. This is in contrast to a third disequilibrium species, GeH4, which shows no evidence for spatial variability. The CRIRES dataset also includes several strong emission lines, which are identified as H3+, an auroral species in Jupiter's ionosphere. The strengths of these lines were measured in order to determine the ionospheric temperatures. The work in this thesis contributes to our understanding of the dynamical, chemical and cloud-forming processes shaping Jupiter's troposphere and provides a reference point for future work, including observations made by NASA's Juno mission.