The multilevel DC-DC converters have advantages of low voltage stress of the switches and diodes and reduction of the filter size. Therefore, such converters are becoming more popular in wide range of application. While multilevel topology offers many new features, it also necessitates a balance control of the capacitors. In the paper a method of capacitor voltage balancing for multilevel isolated DC-DC converters is proposed. The voltage balancing analysis is carried out for a two level converter with input series output parallel structure. The paper describes the operating principles of the balancing circuit, analyzes the fundamental relationships and compares this method with the traditional ones.