Amino acid toxicity is a wide spread phenomenon in biological systems observed in both prokaryotes and eukaryotes. Especially, non-protein amino acids and metabolites can be toxic to humans through food chains. Therefore, development of a simple model assay system for assessing the toxicities of both natural and non-protein amino acids is required and cultured protozoan cells would fulfill the requirements. In this study, we propose the use of green paramecia (Paramecium bursaria) for assessing the acute toxicity of natural amino acids and non-protein N-acetylated amino acid derivatives. The cell survival rates of P. bursaria exposed to solutions of 20 free amino acids and commercially available 16 N-acetylated amino acid derivatives for 12 h of incubation were assessed. The LC₅₀ obtained for natural amino acids are all above mM level. In contrast, we observed that N-acetylation of most amino acids resulted in highly elevated toxicity. Enhancement of toxicity by N-acetylation was observed in glycine, alanine, leucine, proline, aspartic acid, glutamic acid, asparagines, glutamine, cysteine, methionine, phenylalanine, tryptophan, and tyrosine with LC₅₀ ranging between ca. 100 and 200 µM.