High throughput genetic technologies offer the opportunity to gain precision in the diagnosis of numerous diseases and to better understand their molecular basis. However they bring new practical and ethical challenges, some of which are foreseeable and therefore amenable to the timely adoption of strategies to ensure that they are introduced and used in a just and beneficial manner. One way of foreseeing these challenges is to examine technologies that have already been transferred from research to the clinical setting in order to identify the ethical issues and develop strategies to move forward in an ethical way. One such model for new genetic technologies is Array Comparative Genomic Hybridization (aCGH), which has been gradually adopted in recent years as a standard technique in clinical genetics. CGH challenging current clinical practice regarding the detection and diagnosis of human chromosome abnormalities in intellectual disability (ID) and congenital malformations in children. Experience with aCGH has shown that it delivers an unprecedented volume of information for patients, counsellors, and health care providers but it also raises specific ethical challenges which can serve as signposts for potential issues with future, even more detailed, genetic technologies. These issues are described and illustrated through case histories, and their consequences for the patient-clinician relationship in genetic consultation are discussed. The consequences of employing this technology, as compared to the more traditional genetic diagnostic methods used in cases of intellectual disability are categorised into issues linked to 1) the vulnerable nature of patients who are mostly children, mentally retarded people or “future parents”; 2) the way in which information is controlled at each stage of the process, as a function of its potential relevance to the clinical condition being diagnosed, 3) the information related to conditions other than ID or “incidental findings” that become the rule with high throughput technologies. The issues highlighted by the clinical scenarios discussed here can be expected to occur with even greater frequency in the future as whole exome and whole genome sequencing are introduced. Building on our experience with the transfer and adoption of aCGH into clinical genetics, we have developed a grid of points to be considered when translating such technologies from research to clinic.