The duodenal perfusion technique was used to determine whether small peptides were more effective than free amino acids (FAA) for milk protein synthesis and to investigate the effects of infusing soyabean small peptides (SSP) or their FAA on the mammary amino acid (AA) metabolism of lactating goats. Six Saanen goats with silicon catheters implanted into their carotid artery and mammary veins were used in a Latin square design. Blood samples were collected from the carotid artery and mammary vein. The AA concentrations in the plasma, as well as mammary AA uptakes were monitored. The results showed that the concentrations of most essential amino acids (EAA) were significantly higher (P<0.05) in the FAA infusion treatment as compared with the SSP treatment, except for Val, Ile, and Met. The concentration of most of the non-essential amino acids (NEAA), measured after FAA infusion, was highest (P<0.05) when compared with the SSP treatment and the controls. The mammary uptake of most of EAA in the FAA infusion group was higher in comparison with the SSP infusion group. The mammary uptake to milk output ratios of EAA (except for Met) were low in the SSP treatment, compared with the FAA treatment. Significant increases in milk protein yield and milk protein content in the FAA infusion treatment were observed (P<0.05). In the SSP infusion treatment, milk yield and milk protein were numerically increased compared with the control. The abundance of aminopeptidase N (APN) mRNA in mammary tissue was 38.28 in the SSP infusion group, and 2.83, 5.28 in the control and FAA infusion treatment, respectively. In conclusion, the data suggest the FAA was more effective for milk protein synthesis, while the activity of APN was related to utilization of small peptides by the mammary gland.