The indolo[2,1- b]quinazoline alkaloid tryptanthrin has recently been identified as a pharmacologically active compound in Isatis tinctoria, with potent dual inhibitory activity on prostaglandin and leukotriene synthesis. To investigate the skin penetration of tryptanthrin from solutions of pure compound and Isatis extracts, we developed and validated a cutaneous microdialysis model using ex vivo pig foreleg. Microdialysis was performed by placing linear probes in the dermis of the skin in situ, and tryptanthrin concentrations in the dialysates were determined by isotope dilution electrospray ionization LC-MS in the selected ion mode. Measurable concentrations of tryptanthrin were detected 30 min after application. A dose-dependent increase in tryptanthrin concentrations in the dialysate was observed for the Isatis extracts, but not for pure tryptanthrin. Microscopic analysis showed that the pure compound crystallized from the solution but remained in an amorphous state in the extracts.