The roots and leaves of Isatis indigotica, named 'Ban-Lan-Gen' and 'Da-Qing-Ye', respectively, are widely used for the treatment of influenza, viral pneumonia, mumps, pharyngitis, and hepatitis. The indoxyl derivatives detected in the roots and leaves of I. indigotica have been reported to be biologically active. In the present study, a liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method was developed to determine indican, isatin, indirubin and indigotin in the roots and leaves of I. indigotica. The method has been validated for linearity, precision and accuracy. Using multiple reaction monitoring (MRM), the limits of detection (LODs) were determined as 0.004 ng for indican, 0.01 ng for isatin, 0.01 ng for indrubin and 0.03 ng for indigotin, while the limits of quantitation (LOQs) were 0.015 ng for indican, 0.04 ng for isatin, 0.04 ng for indirubin and 0.1 ng for indigotin. Compared with previously reported methods, the current method is more rapid, selective and sensitive. This is the first report of the LC/MS/MS determination of indican, isatin, indirubin and indigotin.