The aim of this study is the three-dimensional structural characterization of the genome packaging inside viral capsids via cryo-electron microscopy and three-dimensional reconstruction. The genome of some single-stranded viruses can be densely packaged within their capsid shells. Several stretches of the genome are known to adopt stable secondary structures, however, to date, little is known about the three-dimensional organization of the genome inside their capsid shells. Two techniques have been developed to facilitate the structural elucidation of genome packaging: the asymmetric random-model method, and the symmetry-mismatch, random model method. Both techniques were successfully tested with model and experimental data. The new algorithms were applied to study the genome structure of poliovirus and satellite tobacco mosaic virus. We have not yet found a consistent structure for the two genomes. Nevertheless, we have found that the genome of satellite tobacco mosaic genome is very stable, supporting a model where the RNA acts as a scaffold, with potential implications in capsid stability and assembly.