This study determines the mean concentrations of free amino acids in stimulated and unstimulated whole saliva in healthy young adults. Standardised salivary amino acids as a substitute for their counterpart in blood, searched for the source of free amino acids in saliva, the probable correlation between particular amino acids with caries experience. Stimulated and unstimulated whole saliva were collected by the draining method in 31 dental students. Saliva was purified, and amino acids were separated by high-performance liquid chromatography. DMFT scores were recorded, and the relation of amino acids to caries experience was explored by generalised linear model. Almost all amino acids had higher concentration in unstimulated whole saliva than in stimulated saliva. The normal range of amino acids (95% CI) and their natural logarithm were defined. There was a significant relationship between caries experience and threonine (P < 0·008), citrulline (P < 0·023) and ornithine (P < 0·001) as a detrimental factor, whereas serin (P < 0·026), glutamine (P < 0·015) and phenylalanine (P < 0·014) had an inhibiting effect on caries. However, in comparison, salivary flow rate (P < 0·013) was a more preventive factor than amino acids. Amino acids in saliva contribute as a marker, instead of their counterpart in blood. Unstimulated saliva had higher concentration of amino acids. Amino acids have different impact on caries and may be one of underlying risk factors for caries experience.