Introduction: Noninvasive prenatal testing (NIPT) is a screening test for fetal aneuploidy with higher specificity and sensibility rates compared to traditional biochemical prenatal screening. Objective: To evaluate concordance between NIPT and prenatal karyotyping testing for detecting fetal aneuploidies in pregnancies with high risk of such disorders. Materials and methods: Prospective pilot study conducted between September 2019 and December 2020 in 20 pregnant patients classified as high risk of aneuploidy based on ultrasound findings and treated in Bogotá and Medellín, Colombia. Each patient underwent a confirmatory invasive test (karyotyping) and a NIPT and an invasive confirmatory test (prenatal karyotyping). Concordance between both methods was determined using Cohen's kappa coefficient (significance level p0.7 were considered as a good level of agreement. Results: Aneuploidies were detected in 3 of the 20 pregnancies (15%) by means of invasive cytogenetic testing, namely, trisomy 21, trisomy 18, and monosomy X. NIPT detected the trisomy 21 and monosomy X cases but failed to detect trisomy 18. Regarding the concordance analysis between NIPT and prenatal karyotype testing in the detection of aneuploidies, Cohen's kappa coefficient was 0.77. As for their concordance for the detection of trisomy 21 and X monosomy, Cohen's kappa coefficient was 1.0, while it was 0 for the detection of trisomy 18. In addition, NIPT detected 67% of aneuploidies. Conclusion: The results of this study, the first of its kind to be conducted in Colombia, showed good concordance between NIPT and prenatal invasive testing (karyotyping) for detecting fetal aneuploidies. However, the results obtained stress the recommendation of using NIPT only as a screening test and not as a diagnostic test.