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This study aimed to determine the correlation between amino acid profiling of a 3-day-old embryo culture medium and embryo implantation potential in women undergoing in vitro fertilization (IVF). The data of 98 patients who received IVF treatment in our hospital from December 2015 to February 2017 were retrospectively analyzed. The 98 patients were grouped into a pregnant group (gemellary pregnancy), a non-pregnant group (non-pregnancy), and a blank control group. The amino acids from a 3-day-old embryo culture medium and blank control medium were collected and were analyzed using high performance liquid chromatography (HPLC). The HPLC results showed that amino acids including aspartate (ASP), serine (SER), glycine (GLY), histidine (HIS), taurine (TAU), arginine (ARG), threonine (THR), alanine (ALA), and proline (PRO) were detected in the 3-day-old embryo culture medium and blank control medium. There are significant differences between the pregnant group and non-pregnant group in peak height (H)-SER, surface area (S)-ASP, S-SER, S-HIS, and S-ALA. The discrimination analysis according to the peak height and peak area of amino acids revealed that the prediction rate of the pregnant group, non-pregnant group, and blank control group were 82.7, 95.7, and 100%. Further, by using the principal component analysis, we found that the prediction rate in these three groups were 90.4, 91.3, and 100%. Our data may suggest that using amino acid concentrations for principal component analysis and discriminant analysis has high accuracy in predicting the relationship between amino acid fingerprint and embryo implantation potential.