Pulsed laser deposition of high Tc compounds onto unheated substrates, resulting in amorphous thin films, preserves to a great extent the composition of matter ejected from the target. This composition is of primary interest, both for understanding the dynamics of laser–target interaction and for practical (optimization) reasons. We have investigated the structure of amorphous and crystalline YBaCuO films obtained both in on-axis and off-axis deposition geometries, and correlated the results with optical and transport properties of these films. X-ray scattering reveals in amorphous films the existence of: (i) amorphous continuum of spatially disordered atoms, (ii) small (10–40 Å) amorphous clusters which can be considered as mesoscopic order fluctuations in the amorphous continuum, and (iii) slightly larger (50–250 Å) crystalline clusters exhibiting quasi-two dimensional (00l) or (11l) long range order. Crystalline films are predominantly (00l) oriented. Optical spectra of both crystalline and amorphous films show regions of enhanced attenuation caused by free charge carriers. Spectra of amorphous samples containing small crystalline clusters exhibit features which we relate to the electron localization caused by quantum size effects. Transport measurements are in good agreement with the structural and optical results. Conductivity of the on-axis films is 3–4 orders of magnitude higher than that of the off-axis films. The (nonlinear) conductivity of amorphous films increases with temperature and remains constant below 200 K. We suggest that besides the usual variable range hopping conduction mechanism, classical tunneling of charge carriers at constant energy between metallic (crystalline) clusters is present. Interestingly, the amorphous off-axis films exhibit a periodic repetition of the elements of atomic order or disorder along the direction of the plasma plume and undergo a structural transition of (11l)→(00l) type.