Atlantic Mackerel (Scomber scombrus) fillets were hot-smoked using an AFOS-Torry Mini Kiln. The nutritional quality of both smoked and nonsmoked fish protein prepared from the same lot of fish, and of a standard protein casein, were evaluated by protein efficiency ratio (PER) in male rats. The hot smoking process caused a significant (p 0.05) decrease in PER of protein from smoked mackerel muscle as compared with that from nonsmoked fish muscle. The change in protein quality was related to the loss of essential amino acids such as lysine and tryptophan and a reduced availability of lysine from smoked fish. Determination of lysine and tryptophan in three layers of the fillet (innermost, middle and outermost) showed that the maximum loss of these amino acids from smoking was in the outermost layer. Lysine and tryptophan were determined by high performance liquid chromatography and spectrophotometric methods, respectively. A small percentage of rats showed some evidence of pale liver on diets containing either casein or smoked mackerel.