Objectives This study characterizes cytogenetic abnormalities with ultrasound findings to refine counseling following negative cell‐free DNA (cfDNA). Methods A retrospective cohort of pregnancies with chromosome abnormalities and ultrasound findings was examined to determine the residual risk following negative cfDNA. Cytogenetic data was categorized as cfDNA detectable for aneuploidies of chromosomes 13, 18, 21, X, or Y or non‐cfDNA detectable for other chromosome abnormalities. Ultrasound reports were categorized as structural anomaly, nuchal translucency (NT) ≥3.0 mm, or other “soft markers”. Results were compared using chi squared and Fishers exact tests. Results Of the 498 fetuses with cytogenetic abnormalities and ultrasound findings, 16.3% (81/498) had non‐cfDNA detectable results. In the first, second, and third trimesters, 12.4% (32/259), 19.5% (42/215), and 29.2% (7/24) had non‐cfDNA detectable results respectively. The first trimester non‐cfDNA detectable results reduced to 7.7% (19/246) if triploidy was detectable by cfDNA testing. For isolated first trimester NT of 3.0–3.49 mm, 15.8% (6/38) had non‐cfDNA detectable results, while for NT ≥3.5 mm, it was 12.3% (20/162). For cystic hygroma, 4.3% (4/94) had non‐cfDNA detectable results. Conclusions Counseling for residual risk following cfDNA in the presence of an ultrasound finding is impacted by gestational age, ultrasound finding, and cfDNA detection of triploidy. What is already known already known about this topic? Maternal serum screening for aneuploidies has changed since the introduction of cell‐free DNA (cfDNA) in 2011. Diagnostic testing with chorionic villus sampling or amniocentesis is recommended in the presence of a structural ultrasound finding. What does this study add? When ultrasound findings are present, the rate of cytogenetic anomalies not detectible by cfDNA increases with increasing fetal gestational age. The size of first trimester nuchal translucency is inversely related to the likelihood of cfDNA detected aneuploidy. 16.3% of cytogenetic abnormalities would likely be missed by cfDNA in the presence of an ultrasound finding.