The study was perform to compare the output of two different docking programs (Molegro Vritual Docker and AutoDock) in simulation of ligand-receptor interactions for β1 and β2 adrenergic receptors. The exactness of the predicted ligand positions was estimated on the basis of the thirteen known crystallographic structures of the ligand-receptor complexes taken from the PDB database. Significant differences in docking results obtained by using both tested programs were observed. The overall RMSD-based scoring suggests that the procedures and algorithms implemented in AutoDock lead to slightly better results.