What's already known about this topic? Current professional guidelines regarding the use of chromosomal microarray analysis (CMA) versus karyotyping in prenatal diagnosis support CMA over karyotype only when fetal structural abnormalities are present. Examination of the clinical utility of these guidelines, given advances in microarray technology and prenatal screening, is largely unaddressed. What does this study add? This study demonstrates the diagnostic superiority of CMA by SNP microarray compared with karyotyping for prenatal diagnosis, regardless of the clinical indication for testing. Objective The American College of Obstetricians and Gynecologists (ACOG) and Society for Maternal‐Fetal Medicine (SMFM) recommend chromosomal microarray analysis (CMA) for prenatal diagnosis in cases with 1 or more fetal structural abnormalities. For patients who elect prenatal diagnosis and have a structurally normal fetus, either microarray or karyotype is recommended. This study evaluates the frequency of clinically significant chromosomal abnormalities (CSCA) that would have been missed if all patients offered the choice between CMA and karyotyping chose karyotyping. Methods A total of 3223 prenatal samples undergoing CMA were evaluated. Cases were categorized into 2 groups: those that met ACOG guidelines for CMA versus those that met ACOG guidelines for either CMA or karyotype. Results Of the 3223 cases, 1475 (45.8%) met ACOG recommendations for CMA, and 1748 (54.2%) met recommendations for either CMA or karyotype. In patients who could have elected either CMA or karyotype, 2.5% had CSCA that would have been missed if the patient had elected to pursue karyotype. Conclusion This study suggests that 2.5% of patients will have a CSCA that may be missed if the guidelines continue to suggest that CMA and karyotyping have equivalent diagnostic value for patients without a fetal structural abnormality.