In this work, we have combined scanning tunneling microscopy (STM) with highresolution transmission electron microscopy (HR-TEM) to investigate the initial stages of Mn deposition on Ge(001) surfaces. The growth temperature has been chosen to be (353 ± 5) K, which is typical for the synthesis of Ge 1−x Mn x thin films. At the early stage of the Mn deposition, two distinct kinds of islands are observed even for Mn coverage much smaller than a monolayer with an average size of respectively 1-2 nm and 4-5 nm. Small islands were found to nucleate in the hollow between the Ge dimer rows and they were formed by consuming Ge from two adjacent rows. This indicates that Mn-Ge alloying has been taken place even at the early stage of the Mn deposition. When the Mn coverage increases, coarsening between small islands with newly deposited ad-atoms occurs, giving rise to the formation of monosized islands. Interestingly, these nanostructures have an average size of 4-5 nm and separated by a spacing of 7-8 nm that are similar to the spatial ordering of nanocolumns resulting from spinodal decomposition in (Ge,Mn) thin films. HR-TEM analyses indicate that those 1 nanoislands are epitaxial, defect free and perfectly coherent with the Ge substrate. A subsequent anneal will result in the formation of Mn 5 Ge 3 islands.