Objective To examine early and late pregnancy loss in women with and without polycystic ovary syndrome (PCOS) undergoing IVF/ICSI transfers. Design Retrospective cohort study. Setting Reproductive medicine center at a tertiary hospital. Population Records were reviewed for women with a positive β-hCG after IVF/ICSI treatment from May 2014 to April 2019. Methods Odds ratios (ORs) for early (13 ≤weeks) and late (13-24 weeks) pregnancy loss were calculated among women with and without PCOS for plurality of the pregnancy with adjustment for confounding factors. Main outcomes measures Early and late pregnancy loss. Results A total of 21,820 charts identified with a positive β-hCG, 2,357 (10.8%) subjects had PCOS, and 19,463 (89.2%) controls did not. Early pregnancy loss occurred in 12.4% of women with PCOS versus 12.8% in women with non-PCOS. Women with PCOS demonstrated a higher rate of late pregnancy loss (5.4% in PCOS vs 3.1% in non-PCOS, OR 1.79, 95%CI, 1.46-2.19, P<.001), regardless of the plurality of the pregnancy (one gestational sac: 4.1 vs. 2.7 percent, OR 1.56, 95%CI,1.18-2.05; ≥ two gestational sacs: 8.1 vs. 4.1 percent, OR 2.08, 95%CI,1.54-2.82, PCOS vs. Non-PCOS, respectively). Potential negative impact of PCOS was reduced to marginal level once BMI were taken into account (aOR 1.42, 95% CI, .99-2.03). BMI and maternal comorbidities were independently associated with late pregnancy loss (aOR 1.65, 95%CI, 1.26-2.17 and aOR 2.07,95%CI,1.43-3.00). Conclusions PCOS women with overweight and preexisting comorbidities would benefit from lifestyle intervention and close surveillance throughout the whole pregnancy.