A key aspect governing spatio-temporal activity patterns in fMRI is the brain state, particularly in animals being imaged mostly during sedation or anesthesia. Two main brain states have been recently identified in rodents, a persistent state similar to awake conditions, and a slow wave state characterized by spontaneous slow oscillation-associated slow wave activity. We analyzed the brain functional connectivity using spontaneous BOLD recordings in rats during these different states. We found that both states lead to differential functional connectivity patterns that can be clearly dissociated. These results are crucial for interpreting rodent studies in the framework of translational resting state research.