The determination of the amino acids proline, histidine, tyrosine, arginine, phenylalanine and tryptophan using flow injection analysis (FIA) with chemiluminescence detection is described. Proline was the only amino acid to exhibit chemiluminescence with the tris(2,2-bipyridyl)ruthenium(III) reaction at pH 10. While, histidine was found to selectively enhance the reaction of luminol with Mn(II) salts in a basic medium. Acidic potassium permanganate chemiluminescence was able to selectively determine tyrosine at pH 6.75. Low pressure separations using a C18 guard column allowed the simultaneous determination of tyrosine and tryptophan or phenylalanine and tryptophan with acidic potassium permanganate and copper(II)–amino acid–hydrogen peroxide chemiluminescence, respectively. Precision for each method was less than 3.9% (R.S.D.) for five replicates of a standard (1×10−5 M) and the detection limits ranged between 4×10−9 and 7×10−6 M. Preliminary investigations revealed that the methodology developed was able to selectively determine the individual amino acids in an equimolar mixture of the 20 naturally occurring amino acids.