As scaling is more and more aggressive, intermittent faults are increasing their importance in current deep submicron complementary metal-oxide-semiconductor (CMOS) technologies. This work shows the dependability assessment of a fault-tolerant computer system against intermittent faults. The applied methodology lies in VHDL-based fault injection, which allows the assessment in early design phases, together with a high level of observability and controllability. The evaluated system is a duplex microcontroller system with cold stand-by sparing. A wide set of intermittent fault models have been injected, and from the simulation traces, coverages and latencies have been measured. Markov models for this system have been generated and some dependability functions, such as reliability and safety, have been calculated. From these results, some enhancements of detection and recovery mechanisms have been suggested. The methodology presented is general to any fault-tolerant computer system.