Jupiter’s atmosphere has been sounded in transmission from the UV to the IR, as if it were a transiting exoplanet, by observing Ganymede while passing through Jupiter’s shadow. The spectra show strong extinction due to the presence of aerosols and haze in Jupiter’s atmosphere and strong absorption features of methane. Here, we report a new detailed analysis of these observations, with special emphasis on the retrievals of the vertical distribution of the aerosols and their sizes, and the properties and distribution of the stratospheric water ice. Our analysis suggests the presence of aerosols near the equator in the altitude range of 100 hPa up to at least 0.01 hPa, with a layer of small particles (mean radius of 0.1 μm) in the upper part (above 0.1 hPa), an intermediate layer of aerosols with a radius of 0.3 μm, extending between ∼10 and 0.01 hPa, and a layer with larger sizes of ∼0.6 μm at approximately 100–1 hPa. The corresponding loads for each layer are ∼2 × 10‑7 g cm‑2, ∼3.4 × 10‑7 g cm‑2, and ∼1.5 × 10‑6 g cm‑2, respectively, with a total load of ∼2.0 × 10‑6 g cm‑2. The lower and middle layers agree well with previous measurements; but the finer particles of 0.1 μm above 0.01 hPa have not been reported before. The spectra also show two broad features near 1.5 and 2.0 μm, which we attribute to a layer of very small (∼10 nm) H2O crystalline ice in Jupiter’s lower stratosphere (∼0.5 hPa). While these spectral signatures seem to be unequivocally attributable to crystalline water ice, they require a large amount of water ice to explain the strong absorption features.