Introduction: To estimate the procedure-related risks of pregnancy loss following chorionic villus sampling (CVS) and amniocentesis (AC) compared to pregnancies without procedure. This cohort study enrolled all women who underwent CVS or AC at the Department of Perinatology, University Medical Centre, Ljubljana, Slovenia (from January 2013 to June 2015). For each group we obtained a maternal age and gestational age (11-14 weeks for CVS and >15 weeks for AC) for a matched control group without invasive procedures from the national database. The data was obtained from hospital records and telephone surveys concerning pregnancy outcomes. Pregnancy loss rates in intervention vs. control groups were compared by generating relative risk (RR) with a 95% confidence interval. During the study period, 828 women underwent CVS and 2,164 women underwent AC. Complete outcome data was available in 2,798 cases (93.5%, 770 CVS, 2,028 AC). Pregnancy loss occurred in 8/770 (1.04%, 95% CI 0.4-2.0%) after CVS vs. 15/1130 (1.33%, 95% CI 0.8-2.2%) in matched control (RR 0.8, 95% CI 0.33-1.8, p=0.6). It occurred in 16/2028 (0.79%, 95% CI 0.5-1.3%) after AC vs. 14/395 (3.29%, 95% CI 2.1-5.8%) in matched control (RR 0.2, 95% CI 0.11-0.45, p<0.0001). The pregnancy loss rates after CVS and AC were comparable to losses in pregnancies without these procedures. With the increasing use of non-invasive prenatal testing, information that the invasive procedures are safe when indicated is essential.