Purpose To evaluate the trends in prenatal diagnosis over 26 years in a tertiary referral hospital. Methods A retrospective analysis of invasive prenatal procedures performed between 1991 and 2016. Maternal characteristics, indications for invasive diagnosis, and percentage of abnormal karyotypes were compared between periods according to guidelines implemented nationally and locally. Results A total of 14,302 invasive prenatal procedures were performed. The proportion of invasive procedures performed for advanced maternal age, abnormal karyotype in a previous pregnancy, and maternal anxiety decreased from 71.1%, 17.8%, 8.9% in 1991 to 23.9%, 1.3%, and 2.3% in 2016 (OR 0.6, 0.8, and 0.9 for each 5 years, respectively; p < 0.001), while the proportion of invasive procedures performed for abnormal ultrasound increased from 2.2% in 1991 to 51.6% in 2016 (OR 1.9 for each 5 years; p < 0.001). Abnormal karyotype was found in 9.7%. The proportion of abnormal karyotypes increased significantly from 0.0% in 1991 to 15.7% in 2016 (OR 1.35 for each 5-year period; p < 0.001). The odds of abnormal karyotype increased after the implementation of the Ordinance of the Minister of Health in 2003 (OR 1.6), the National Prenatal Screening Program in 2007 (OR 2.2), and the in-house genetic counseling with combined first trimester screening in 2015 (OR 3.1). Conclusions Significant changes in prenatal diagnosis led to a better selection of patients undergoing invasive prenatal procedures. The implementation of in-house genetic counseling was associated with an increased rate of the detection of abnormal karyotypes.