We have performed first-principles and empirical molecular dynamics calculations of the effect of size and surface reconstruction on the atomic structure properties of small Ge nanoparticles (1–2.5 nm). Systems with ideal H-passivated surfaces, or bare reconstructed surfaces have been considered. We show that the surface reconstruction leads to a very strong volume contraction of the nanoparticles, equivalent to an applied pressure of 4 GPa for a 2 nm nanoparticle. We also found that the surface reconstruction shifts significantly the optic mode peak of the vibrational spectrum, thus preventing a straightforward size determination from Raman spectroscopy.