Modeling a protein structure based on a homologous structure is a standard method in structural biology today. In this process an alignment of a target protein sequence onto the structure of a template(s) is used as input to a program that constructs a 3D model. It has been shown that the most important factor in this process is the correctness of the alignment and the choice of the best template structure(s), while it is generally believed that there are no major differences between the best modeling programs. Therefore, a large number of studies to benchmark the alignment qualities and the selection process have been performed. However, to our knowledge no large-scale benchmark has been performed to evaluate the programs used to transform the alignment to a 3D model. In this study, a benchmark of six different homology modeling programs— Modeller, SegMod/ENCAD, SWISS-MODEL, 3D-JIGSAW, nest, and Builder—is presented. The performance of these programs is evaluated using physiochemical correctness and structural similarity to the correct structure. From our analysis it can be concluded that no single modeling program outperform the others in all tests. However, it is quite clear that three modeling programs, Modeller, nest, and SegMod/ ENCAD, perform better than the others. Interestingly, the fastest and oldest modeling program, SegMod/ ENCAD, performs very well, although it was written more than 10 years ago and has not undergone any development since. It can also be observed that none of the homology modeling programs builds side chains as well as a specialized program (SCWRL), and therefore there should be room for improvement.