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Objectives: To explore the advantages and limitations of comparative genomic hybridization to BAC arrays (array CGH) for prenatal diagnosis of a fetus with anomalies and a chromosome abnormality. Methods: We used karyotype analysis, FISH and array CGH to investigate an unbalanced chromosome rearrangement. Results: We report a case of a fetus with ultrasound anomalies at 11 weeks’ gestation and an unbalanced chromosome translocation [46,XX,der(13)t(2;13)(p25.1;q32)pat]. Initially, a chromosome 13 deletion was reported from G-banded chromosome analysis and 13q subtelomere FISH. The involvement of chromosome 2 was determined after a balanced translocation was identified in the father, 46,XY,t(2;13)(p25.1;q32). Array CGH confirmed the fetal abnormality as partial trisomy of the short arm chromosome 2 and partial monosomy of the long arm of chromosome 13. The abnormalities identified by ultrasound studies and autopsy appear to be most consistent with 13q deletion syndrome. Conclusions: Array CGH successfully identified a subtle unbalanced chromosome complement in a fetus with multiple ultrasound anomalies. If array CGH had been performed along with the fetal karyotype, the cryptic partial trisomy 2 could have been identified in a more timely manner to assist in the prenatal counseling of this family. Copyright © 2008 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]