In this paper we report on the growth and structural characterization of very thin (20 nm) Cr-doped ITO films, deposited at room temperature by double-target pulsed laser ablation on amorphous silica substrates. The role of Cr atoms in the ITO matrix is carefully investigated with increasing doping content by transmission electron microscopy (TEM). Selected-area electron diffraction, conventional bright field and dark field as well as high-resolution TEM analyses, and energy dispersive x-ray spectroscopy demonstrate that (i) crystallization features occur despite the low growth temperature and small thickness, (ii) no chromium or chromium oxide secondary phases are detectable, regardless of the film doping levels, (iii) the films crystallize as crystalline flakes forming large-angle grain boundaries; (iv) the observed flakes consist of crystalline planes with local bending of the crystal lattice. Thickness and compositional information about the films are obtained by Rutherford back-scattering spectrometry. Results are discussed by considering the combined effects of growth temperature, smaller ionic radius of the Cr cation compared with the trivalent In ion, doping level, film thickness, the double-target doping technique and peculiarities of the pulsed laser deposition method.