To examine neuronal activation in the spinal cord due to secondary hyperalgesia resulting from intrajoint capsaicin injection, and the effect of physiotherapy manipulation, using functional magnetic resonance imaging (fMRI), in alpha-chloralose anesthetized rats. FMRI of the rat lumbar spinal cord was performed at 9.4 Tesla. Stimuli included injection of 25 microL of capsaicin (128 microg/mL in 7.5% dimethyl sulfoxide [DMSO]) into the right forepaw or 75 microL into the right ankle joint followed by a light touch stimulus, with and without physiotherapy manipulation. Activation of pain areas of the spinal cord (dorsal horn) was found in all animals after injection of capsaicin into the plantar surface of the rat hindpaw and ankle joint. Overlay maps depicting activations and deactivations showed significant reproducibility between experiments. Greater overlay of activations were observed for intrajoint compared to intradermal capsaicin injection. The distribution of activations after stimulation of the hindpaw using a light touch stimulus was somewhat more varied; activation of the dorsal horn was evident, with greater overlap resulting when joint mobilization was not performed. Results suggest a trend toward decreased areas of activation in the spinal cord associated with pain, as a result of hyperalgesia, following physiotherapy joint mobilization.