A prospective assessment following a step-wise protocol in 281 patients with unexplained cognitive delay was used to assess diagnostic possibilities. Diagnostic procedures were complex and required a multidisciplinary approach. One third of diagnoses was established based on clinical history and physical exam only; for another third, clinical history and physical exam provided essential clues for additional investigations; and a third were established by additional investigations only. The likelihood to reach a diagnosis did not depend on the severity of mental retardation. We found that in a tertiary care center, a diagnosis can be established in 1 out of every 2 patients. Clinical history and physical examination are the most important instruments to reach a diagnosis.