Fetal chromosomes are examined conventionally by G-band karyotyping. More recently Prenatal Chromosomal Microarray (CMA) has been used to look for fetal chromosomal abnormalities. Advantages of CMA include its higher detection rate. Disadvantages include its detection of Variants of Unknown Significance (VOUS). I recruited a prospective cohort of 243 women with structural abnormalities on fetal ultrasound scan. A 1Mb targeted BAC array was performed in addition to G-band karyotyping. In 62 cases from this cohort an additional higher resolution 60K oligonucleotide array was used. A health economic analysis, by use of a decision tree, was performed. Finally qualitative work determined women’s feelings about testing. The 1Mb BAC cohort found a 4.1% increase in fetal chromosomal abnormalities over karyotyping, with a low detection rate of VOUS (0.4%). The 60K sub-cohort noted an extra 4.8% pathogenic chromosomal anomalies but, in addition, a 13% increase in VOUS. The health economic analysis indicated that when CMA is £360 (per test) and the Willingness To Pay (WTP) for a “positive diagnosis” is £9768; then CMA is cost effective over karyotyping. Qualitative analysis showed that couples were keen for as much information as possible. They struggled to recall and retain information conveyed at the time of the testing.