Common mode failures create the major impact on the system reliability in many real time systems. In this paper, we incorporate the concept of common mode faults (CMF) for the reliability prediction of fault tolerant software system consisting of N-version with different failure characteristics. The common mode faults may occur simultaneously in two or more versions due to faults in the common communication buses or shared environmental factors, failure of common source of power, design mistake, etc. The recursive algorithm based on universal generating function approach is presented to obtain the system probabilities. Various performance measures of the fault tolerant software system are established. Furthermore, by setting appropriate parameters, some special cases are illustrated numerically. © Operational Research Society of India 2013.