A rapid, sensitive and selective HPLC separation with photodiode array detection was developed for the analysis of the novel pentacyclic triterpenoid acetyl-11-keto-alpha-boswellic acid. Complete baseline separation of acetyl-11-keto-alpha-boswellic acid from the corresponding isomer acetyl-11-keto-beta-boswellic acid was achieved on a fluorinated stationary phase. The standard curve was linear from 0.98 nmol/l to 196 nmol/l acetyl-11-keto-alpha-boswellic acid. The compound was isolated from chick embryonic plasma using extraction on diatomaceous earth with an overall average extraction yield of 82%. This method was applied in a kinetic study on the chick chorioallantoic membrane model (CAM) and showed unequivocal separation between acetyl-11-keto-alpha-boswellic acid and acetyl-11-keto-beta-boswellic acid unachievable so far.