Various faults may simultaneously occur in a rotor dynamic system. It is crucial to detect and monitor these faults to ensure the safe operation of machinery. Usually, vibration response is utilized for fault diagnosis; however, the identification process becomes more challenging when multiple faults exhibit similar symptoms in the vibration response. In this paper, the vibrational transient response of a cracked rotor is analyzed in the presence of unbalance and coupling misalignment. The study focuses on investigating the possibility, advantages and limitations of using the sub-critical startup response in solving the fault identification problem. Numerical simulations using finite element modeling and experimental investigations are carried out for different individual and multi-fault conditions. Various factors are taken into consideration, including sub-critical limit speed, crack parameters, unbalance parameters and misalignment severity. Numerical and experimental investigations showed that the sub-critical transient response is suitable for the fault detection and diagnosis of the simultaneously existing faults studied. Compared to the critical response, the sub-critical response is more informative and each fault shows a unique feature that can be extracted without the need for sophisticated post signal processing. The study provides useful insights on the interaction between the various fault effects on the vibratory response and presents a simple method for condition monitoring of industrial equipment.