In the United States, all states screen newborns for MSUD through the State's newborn screening program. This allows for early diagnosis and treatment. Unfortunately, many countries do not include MSUD in their screening programs. In these countries, children may die or become severely handicapped before they are diagnosed.

Infants with classic MSUD appear normal at birth with symptoms appearing within 3 to 7 days. In infants with intermediate MSUD, symptoms are milder and may not be apparent as soon. Symptoms include fussiness, lethargy, decreased nursing/feeding, poor weight gain, hypotonia (poor muscle tone) or hypertonia (excessive muscle tension), vomiting, a high-pitched cry, seizures and the characteristic maple syrup smell of the urine-more noticeable in a diaper after it is dried. (This odor can sometimes be detected as early as the first day by swabbing the ear canal of a newborn with classic MSUD.)

If a maple syrup odor is present, or if there is any question regarding the diagnosis of a newborn, the baby should be seen by a physician and tested for MSUD without delay. The diagnosis can be confirmed by BCAA analysis, a blood test that looks at the levels of the 20 amino acids and their relationships to each other. A correct diagnosis requires the experience of someone trained in metabolic diseases.

At times the peculiar maple syrup smell in the urine or sweat can occur in older, healthy children or adults who are non-symptomatic. The reason for this is unknown. However, these persons should be checked for a milder form of MSUD, especially if there are other symptoms of MSUD.