The free amino acid content of 61 honey samples from Estonia has been determined by HPLC-UV with precolumn derivatization with diethyl ethoxymethylenemalonate. Analyzed samples were seven types of unifloral honeys and polyfloral honeys. The main amino acids found in Estonian honeys were proline and phenylalanine. The resulting data have been analyzed by t test and principal component analysis (PCA). t Test revealed that some amino acids (alpha-alanine, beta-alanine, asparagine, gamma-aminobutyric acid, glutamine, glycine, histidine, ornithine, phenylalanine, proline, serine, and tryptophan) are more potent for assigning honey botanical origin than others. PCA enabled differentiation of some honey types by their botanical origin. In the space of the two first principal components, heather honeys form a cluster that is clearly separable from, for example, polyfloral honeys. It is concluded that analysis of the free amino acid profile may serve as a useful tool to assess the botanical origin of Estonian honeys.