Objective:To evaluate the detection of copy number variation (CNV) by chromosome microarray analysis (CMA) in fetuses with congenital anomalies of the kidney and urinary tract (CAKUT).Methods:A total of 1 929 fetuses who were ultrasonically found with CAKUT and underwent CMA from Guangdong Women and Children's Hospital and Health Institute were enrolled in this retrospective study from January 2016 to July 2020. These fetuses were divided into isolated CAKUT group ( n=1 567), CAKUT with soft markers group ( n=269), and CAKUT with other structural anomalies group ( n=93) for comparing the detection rate of pathogenic CNV using Chi-square test or Fisher exact test. Results:(1)The detection rate of all and pathogenic CNVs were 6.5%(125/1 929) and 4.8%(93/1 929), respectively. The total detection rate of CNV, clinically significant CNV and large chromosome structural variations in the CAKUT with other structural anomalies group were higher than those of the CAKUT with soft markers group and isolated CAKUT groups[31.2%(29/93), 11.5%(31/269) vs 4.2%(65/1 567), χ2=119.002; 18.3%(17/93), 9.0%(24/269) vs 3.6%(56/1 567), χ2=49.677; 9.7%(9/93), 2.2%(6/269) vs 0.3%(4/1 567), χ2=42.727; all P<0.001]. CAKUT with other structural anomalies group had a higher detection rate of pathogenic CNV (18.3%, 17/93) than the CAKUT with soft markers group (8.6%, 23/269) and the isolated CAKUT group [3.4%(53/1 567)] ( χ2=51.932, P<0.001). (2) The detection rate of pathogenic CNV was the highest in fetuses with enhanced renal echo (14.7%, 23/156), followed by renal enlargement (8.2%, 5/61), renal dysplasia (5.0%,13/261), polycystic renal dysplasia (5.0%, 13/261), and hydronephrosis (4.8%, 20/413). Fetuses with polycystic renal dysplasia, renal agenesis, fused kidney and hydronephrosis in the CAKUT with other structural anomalies group had a higher detection rate of pathogenic CNV than those in the isolated CAKUT group [3/9 vs 3.5%(8/230), 2/17 vs 1.3%(3/237), 1/8 vs 0.0%(0/59) and 3/18 vs 3.4%(12/344), all P<0.017]. The CAKUT with other structural anomalies group had a higher detection rate of pathogenic CNV than CAKUT with soft markers group in fetuses with enhanced renal echo [4/8 vs 12.8%(5/39), P<0.017]. (3) The top three microdeletion/microduplication syndrome were 17q12 microdeletion syndrome (36.6%, 34/93), 22q11.2 microdeletion syndrome (23.7%, 22/93), and 16p11.2 microdeletion syndrome (7.5%, 7/93) among those with pathogenic CNV. Conclusions:The risk of CNV in fetuses with isolated CAKUT, CAKUT with soft markers, and CAKUT with additional structural anomalies increased progressively. CMA might be a better choice in fetuses with hydronephrosis, enhanced renal echo, renal enlargement, renal hypoplasia, and multicystic renal dysplasia to improve the detection rate of CNV.