A major application of array comparative genomic hybridization (aCGH) is to define a specific cause in children with undiagnosed learning and developmental disability (LDD). Medical notes for 46 consecutive patients selected for aCGH analysis by clinical dysmorphologists were abstracted for clinical investigations related to LDD and a cost-consequences analysis was performed. aCGH analysis was completed in 36 cases and five diagnostic chromosomal anomalies were identified (13.8%). The number of investigations undertaken on each child varied. With aCGH estimated to cost £590 per case, if aCGH had been undertaken after negative standard initial tests for LDD investigation, the additional cost would be £2399 per positive case. If the cost of aCGH was reduced to £256 per case (∼€350), aCGH becomes cost neutral. All chromosomal anomalies detected by aCGH had a de Vries score of ≥5. If aCGH had only been used for individuals with a score of ≥5, the sensitivity increased to 21.7% yielding a cost of £1087 per positive case identified. Pre-selection of cases for aCGH based on de Vries criteria has a major economic impact on introducing aCGH into clinical practice. Prospective studies are required to explore the long-term costs and consequences of aCGH and identify when aCGH may provide the most benefit at least cost.