Invasive prenatal testing (IPT) by amniocentesis (AMN) or chorionic villus sampling (CVS) are relative common in centralised fetal diagnostic centres. Pain perception is a usual concern for patients and may affect the final decision process. The aim of this study was to identify modifiable factors associated to the patients' perception of pain. In patients scheduled for IPT to our referral centre we prospectively determined the immediate pos procedure pain perception through an analogue pain perception scale 1 to 10. We analysed the referred score of pain perception with the following factors: patient demographics, indication, access for CVS, number of attempts, operator experience, puncture site for AMN and patients body mass index. Statistical analysis was performed using appropriated tests. A p-value of < 0.05 was considered statistically significant. 431 cases of IPT were practiced between 2018 and 2020. Procedures were practiced by 5 operators. The choice between AMN, CVS either transabdominal (TA CVS) or transcervical (TC CVS), were gestational age (GA), placental localisation and operators' choice. The pregnancy loss rate was 0.5%. 391 (90.7%) patients underwent AMN and 40 (9.3%) CVS. For the AMN group the median age was 34 years (IQR 29-39), median GA was of 19 weeks (IQR 16-24), perception of pain was higher in obese patients, lateral needle insertion and in patients which procedure was performed by the operator with the less annual number of procedures. On logistic regression, location of needle insertion and individual operators number of procedures were shown as predictive factors for higher pain perception. For CVS the median age was 34 years (IQR 31-39), median GA was 13.2 weeks (IQR 12-14), and perception of pain was significantly higher in patients with TA CVS (p < 0.001). Identification and modification of pain related factors may diminish the discomfort for the patient as well as procedure related anxiety and should be included in patient counselling.