Cinnamaldehyde (CA), an active ingredient isolated from the traditional Chinese medicine Cortex Cinnamomi, has a wide range of bioactivities. To clarify the distribution characteristics of CA, a selective and sensitive method utilizing gas chromatography-mass spetrometry was initially developed for simultaneously determining the concentration of CA and its metabolite cinnamyl alcohol in rat tissues. Selected ion masses of m/z 131, 105 and 92 were chosen, and separation of the analytes was performed on a DB-5 ms (30 m × 0.25 mm, 0.25 µm, thickness) capillary column by gas chromatography-mass spectrometry. The calibration curves demonstrated good linearity and reproducibility over the range of 20-2000 and 20-4000 ng/mL for various tissue samples. Recoveries ranged from 86.8 to 107.5%, while intra- and interday relative standard deviations were all <11.3%. The analysis method was successfully applied in tissue distribution studies for CA and cinnamyl alcohol. As CA and cinnamyl alcohol may inter-convert to one another, simultaneous determination of both analytes provides a comparative and accurate data for tissue study. The concentrations of CA and cinnamyl alcohol remaining in spleen were the highest among the main organs, including heart, liver, spleen, lung, kidney and brain. In addition, there was no long-term accumulation of CA in rat tissues.