Purpose The study was designed to investigate the effect of vitrification and slow freezing for the cryopreservation of human day 3 embryos on serum β-hCG levels in pregnancies established after frozen embryo transfer (FET). Methods Of the 1384 FET cycles initiated, 1131 embryo transfers met study criteria and assigned to one of two groups: 797 slow-freezing embryo transfers or 334 vitrified embryo transfers. Median values of β-hCG and outcome of all pregnancies were compared between the two groups. Predictive values of serum β-hCG on day 12 after embryo transfer for establishing ongoing pregnancy and pregnancy failure were determined by receiver operating characteristic (ROC) curve analysis. Results In the slow-freezing group, 383 ongoing pregnancies occurred (48.1 %), and transfers of vitrified embryos resulted in 154 pregnancies (46.1 %). Median β-hCG values (279.2 IU/L) for ongoing pregnancies after transfer of vitrified embryos were significantly lower than that of slow frozen embryos (320.5 IU/L). The median values of β-hCG for singleton in the two groups was statistically significant (P<0.05). For slowfreezing embryo transfers, the cut-off value of β-hCG in predicting ongoing pregnancy was 147 IU/L (sensitivity 88.3 %, specificity 80.7 %). For vitrified embryo transfers, the value was 135 IU/L (sensitivity 84.4 %, specificity 76.3 %). Conclusions Day 12 β-hCG levels after FET are significantly affected by the methods of embryo cryopreservation for ongoing pregnancies. Furthermore, when using β-hCG cutoff value to assess pregnancy outcome, the cryopreservation methods should be taken into account.