The compounds formed in fish spoilage process have been frequently used to assess the quality of different species. Quality indices based mainly on the concentration of the products of nucleotide degradation and biogenic amine content have been proposed. However, these indicators must be calculated considering intrinsic and extrinsic factors that may affect both, biogenic amine formation and nucleotide degradation rate and pattern. In relation to the analytical methods, regardless the methodology chosen, the extraction stage is critical. High performance liquid chromatography is the technique indicated for both, biogenic amine analysis and determination of nucleotide degradation products.