Free amino acids (FAAs) and nucleotide-related compounds in white muscle, dark muscle, and the viscera of milkfish (Chanos chanos) were analyzed by an automatic amino acid analyzer and high-performance liquid chromatography. Histidine was the most prominent FAA in milkfish white muscle, accounting for 63% of the total FAAs. In dark muscle, histidine accounted for 33%, and taurine, 38%. The most abundant FAA in the viscera was taurine followed by glutamic acid, alanine, and histidine. The viscera contained a much lower amount of histidine than both muscles. Inosine 5‘-monophosphate (IMP) was the major nucleotide compound in white muscle and its level was about 3 times higher than that in dark muscle. The IMP level in the viscera was far less than those in muscles; however, the viscera contained more hypoxanthine and xanthine. Keywords: Milkfish; free amino acids; histidine; nucleotides; muscles; viscera