A new method for the concurrent extraction and quantification of tryptophan (Trp), tryptamine (T), indole-3-acetic acid (IAA), serotonin (5-HT) and 5-hydroxyindole-3-acetic acid (5-HIAA) in samples of rat brain is presented. Homogenization is carried out in 0.1 N HCl containing 1 N KCl and 0.2% NaHSO3. After centrifugation at 100,000g, the supernatant is percolated through a column of XAD-2 resin, eluted with distilled methanol and the resulting eluate is evaporated to dryness. The dry residue is then derivatized to yield the pentafluoropropionated (PFP) and methylpentafluoropropionated (Me-PFP) derivatives. Identification and quantification is readily achieved by gas chromatography-mass fragmentographic analysis on a OV-17 or Dexsil 300 column. Endogenous levels in whole rat brain established by this method are IAA, 13,1 .+-. 2.0 ng/g (n = 6); T, < 380 pg/g (n = 6); Trp; 4.16 .+-. 0.23 .mu.g/g (n = 6); 5-HIAA, 442 .+-. 24 ng/g (n = 6); and 5-HT, 526 .+-. 81 ng/g (n = 5).