Fermented seeds of the tropical tree Pangium edule Reinw, are a speciality in Indonesia and have been used as spices. The fermentation process of the seeds is a natural spontaneous process, which occurs 40 days following seed maturity and treatment. This study reports some biochemical changes, especially primary metabolites. and antioxidant activity associated with mobilization of lipids and phenolics during seed fermentation. The lipid content increased slightly (46.07-50.95% db) although the dominant fatty acid composition did not change. The dominant fatty acids were oleic acid (C-18:1 n-9) and linoleic acid (C-18:2 n-6). During fermentation, the decrease in fatty acid content in lipid coincided with the increasing acid value, which indicated that free fatty acids increased in seeds during fermentation. The dominant tocol in the seed, gamma-tocotrienol, increased (69.8-123.3 mu g g(-1) freeze-dried seed) during fermentation. In general, overall protein content and amino acid composition did not change but non-soluble protein increased while soluble protein decreased. The changes in carbohydrate fraction showed that total crude carbobydrate, neutral detergent fibre (NDF, as cellulose, hemicellulose, and lignin) decreased, but reducing sugar increased and starch content did not change. Enzyme assays showed that microorganisms may be involved in the fermentation process. beta-glucosidase, an enzyme that can cleave glycosidic bonds of conjugated phenolics and guaiacol peroxidase (GPX) activities increased. The total phenolics content in seeds increased substantially corresponding to the increase in beta-glucosidase but antioxidant activity of phenolic extracts did not change.