A series of N-trifluoroacetyl/pentafluoropropionyl-O-trifluoroethyl/ pentafluoropropyl/heptafluorobutyl ester derivatives of 5-methoxyindole-3-acetic acid (5MIAA) were synthesized. Under electron-capture negative ionization conditions, the N-trifluoroacetyl derivatives were found to yield relatively abundant, analyte-specific M-. molecular ions and [M-HF]-., [M-HF-CF2CO]-. and [M-CF3CO]- fragment ions, while the N-pentafluoropropionyl derivatives yielded predominantly the reagent-specific pentafluoroacylium C2F5CO- ion. 5-[2H3]Methoxyindole-3-acetic acid was prepared in high yield by a new synthetic procedure and used as the internal standard in subsequent gas chromatographic/mass spectrometric analysis. Using the N-trifluoroacetyl-O-pentafluoropropyl ester derivative, femtomole to low picomole per gland/organ per g ml-1 levels of endogenous 5MIAA were identified and determined in the rat pineal gland, retina, whole brain and serum.