Objectives: To investigate the prevalence of pathogenic and likely-pathogenic variants detected by chromosomal microarray analysis (CMA), among pregnancies with fetal short long bones diagnosed by ultrasound. Design: A retrospective study. Setting: The study was based on national records from the Israeli Ministry of Health. Sample: Chromosomal microarray analyses performed nationwide, during January 2016 to March 2018, for the indication of prenatal diagnosis of short long bones (n=66). Methods: Clinical data was retrieved from genetic counselling summary letters and from patients’ medical records. The CMA yield was compared to two cohorts that reported the background risk. Main outcome measure: Pathogenic/likely pathogenic CMA. Results: There were 4 cases with a pathogenic/likely pathogenic result (6%). The rate of chromosomal abnormalities was significantly higher compared to the background risk for copy number variations (CNVs) [P<0.001], [odds ratio (OR) 4.5, 95% CI 1.6-12.7], [OR 5.8, 95% CI 2-16.2], for both isolated [OR 6.1, 95% CI 1.4-26], [OR 7.8, 95% CI 1.8-33.5], and non-isolated cases[OR 10, 95% CI 2.2-44], [OR 12.8, 95% CI 2.9-57], , and for cases in which the lowest estimated bone length percentile was above the 3rd percentile (below 5th percentile) [OR 23, 95% CI 6.2-87], [OR 29.9, 95% CI 8-111], . Conclusion: The yield of CMA in cases with short long bones (both isolated and non-isolated) is significantly higher than the background risk for chromosomal anomalies in pregnancies with no sonographic anomalies. This suggests that CMA should be offered in pregnancies with a diagnosis of fetal short long bones.