Film density of amorphous In-Ga-Zn-O (a-IGZO) was varied in a wide range to investigate the origin of the low film density and its effect on thin-film transistor (TFT) characteristics. Device-quality a-IGZO films have the densities ∼ 6.1 g/cm3, which is ∼5% smaller than that of single-crystal InGaZnO4 (c-IGZO) (6.4 g/cm3). On the other hand, extremely low density of 5.5 g/cm3 was obtained when the sputtering working pressure (PTot) was increased to 5 Pa. High density desorption of H2O and O2 was detected in the low-density films, which are attributed to an origin of the low density. Although the low-density channel produced poor TFTs, good TFT characteristics were obtained by annealing at Tann = 300°C. The densities of the low-density films obtained by X-ray reflectivity (XRR) analysis were, however, almost unchanged up to Tann = 500°C, while spectroscopic ellipsometry (SE) analysis showed that densification started from 100°C. This contradiction is explained by transmission electron microscopy (TEM). Although conventional high-resolution TEM (HR-TEM) observation could not detect a microstructure in the high-density a-IGZO films, high-angle annular dark field scanning TEM (HAADF-STEM) detected nano-scale low-density regions. The low-density films had larger and more voids. These void structures were not found in very thin regions (5–10 nm from the substrate surface) but increased in thicker regions.