Functional magnetic resonance imaging (fMRI) has evolved into a method widely used to map neural activation in the human brain. fMRI is a method for recording blood oxygen level-dependent (BOLD) signals. These signals change with local cerebral blood flow coupled to neural activity. However, the relationship between BOLD signals and neural function is poorly understood and requires the development of animal models. Here we use an unanesthetized rat preparation to study BOLD responses to whisker stimulation in somatic sensory barrel cortex. Five rats were trained to tolerate restraint in a holder and fMRI noise with positive reinforcement. For maximal immobilization, the head was fastened to the holder with nuts screwed on threaded bolts attached to the head. On scanning day, residual stress was alleviated with injections of diazepam, and the rats were restrained in the holder and transferred into the scanner. After >75 min to allow the tranquilization to abate, structural images were acquired from three coronal brain slices. Subsequently, functional images were taken utilizing 4-min epochs without stimulation alternated with equivalent epochs during which the right caudal whiskers were stimulated with three air puffs/s. After 4 weeks, fMRI could be repeated in four rats. In seven of the nine functional runs, head motion was minimal and whisker stimulation resulted in a statistically significant (P </= 0.05) increase in BOLD signal in barrel cortex predominantly on the contralateral side. The results provide encouragement that long-term fMRI studies on cerebral function in unanesthetized rats may be feasible with our procedure.