Objective To analyze the molecular genetics changes of multiple malformations using array-based comparative genomic hybridization (aCGH), and evaluate the value of this technique in routine chromosomal karyotype analysis. Methods Thirty one cases were studied of fetal multiple malformations collected by ultrasound examination from Feb. 2012 to May 2015 in General Hospital of Chinese PLA. The age of gravida ranged from 20 to 37, the gestational time ranged from 21 to 27 weeks. Samples of amniotic fluid and umbilical cord blood were collected, and chromosomal karyotype analysis and aCGH were carried out. Results All of 31 samples were successfully detected by G-band chromosomal karyotype analysis and aCGH. Among karyotype analysis, 4 samples failed of cultivation, and 1 showed no karyokinesis. Among 26 cases of successful cultivation, 3 were with abnormal karyotype leading to a abnormality rate of 11.54% (3/26). In the aCGH analysis, the chromosomal polymorphism with no pathogenicity of microdeletion and microduplication were detected in 21 cases; 6 cases showed abnormal and the abnormality rate was 19.35% (6/31). Conclusions Array-based comparative genomic hybridization technique has the advantages of high resolution and wide coverage, may not only make up for the defect of unable to do karyotyping since failed cultivation or lacking cell vigor, but also reveal the microdeletion and microduplication at submicrostructure level, which is favorable for understanding the reason and providing the evidence of fetal malformation. DOI: 10.11855/j.issn.0577-7402.2016.09.10