Abstract The room-temperature growth of Sn on Si(001) is studied from the initial stages of metal adatom adsorption all the way to the formation of three-dimensional clusters. Overall, Sn grows in the Stranski–Krastanov mode. The first atomic layer is an array of Sn adatom dimers showing local 2×2 periodicity. After the completion of this first layer, the nature of the transition between two-dimensional and three-dimensional growth is very complex. Three complete and distinct two-dimensional layers of Sn grow, each with a different surface structure, before there is significant three-dimensional growth of clusters. It is not possible to assign an atomic structure for the second or third atomic layers strictly on the basis of these STM data. The three two-dimensional layers taken together form a three-dimensional structure that has an anomalously low bulk density of atoms; in essence, an “atomic sponge”.