Introduction: We evaluated the contribution of array comparative genomic hybridization (aCGH) to the final diagnosis in children with neurocognitive disturbances or dysmorphic findings, but lacked a specific diagnosis. Materials and methods: Medical files of pediatric patients with neurocognitive disturbances who underwent aCGH analysis were reviewed retrospectively. Results: Of 155 patients, 77 copy number variations were detected and 50% (39/77) were considered causative. The aCGH's final diagnostic rate was 25.1% (39/155). Conclusion: With aCGH analysis, the diagnosis rate for patients with undiagnosed neurocognitive disturbances or dysmorphic syndrome may increase by 25-30%. If the phenotypic findings of the widely known neurocognitive disturbances cannot be identified during the initial clinical assessment, aCGH analysis may be beneficial.