The capillary blood flow parameters recovery is one of the videocapillaroscopy objectives. Capillaries position can vary at recorded video sequences due to the registration features of capillary blood flow. Stabilization algorithm of capillary blood flow video frames based on the advanced phase correlation is proposed and investigated. This algorithm is compared to the advanced version of known algorithms of video frames stabilization based on full-frame superposition and key points detection. Programs based on discussed algorithms are compared by processing of the experimentally recorded video sequences of human capillaries and by processing of computer-simulated video frames sequences with the specified offset. The full-frame superposition algorithm provides high quality of stabilization, however, the program based on this algorithm requires significant computational resources. Software implementation of the key points detection algorithm is characterized by good performance, but provides low quality of stabilization for capillary blood flow video sequences. Algorithm based on phase correlation method provides high quality of stabilization and program realization of this algorithm requires minimal computational resources. It is shown that the phase correlation algorithm is the most useful for stabilization of video sequences for capillaries blood flow. Obtained results can be used in software for biomedical diagnostics.