Phenylketonuria, also known as PKU, is a rare genetic disorder that may cause smelly urine. The smell is often described as "mousy" or "musty" and is usually detected not only in urine, but in body odor and breath as well.

PKU is an inherited genetic disorder that is relatively rare. It makes a baby unable to break down a certain amino acid (phenylalanine) that is common in protein-based foods.
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Because the child cannot break down phenylalanine, it builds up in the blood to toxic levels. This can cause damage to the central nervous system and brain.
Phenylketonuria
Symptoms of PKU

Foul, musty smelling urine is not the only symptom of PKU. Other symptoms include:
Very small head
Mental retardation
Seizures
Jerking movements in the limbs
Rashes
Tremors
Relatively light skin, hair and eye color compared to parents and siblings
Hyperactivity

Developmental delay of cognitive and social skills
Tests for Phenylketonuria

A blood test can determine whether or not a child has PKU. In the United States, this blood test is mandatory for all babies. It is usually performed before the baby even leaves the hospital.
Treatment for Phenylketonuria

A diet extremely low in phenylalanine is the most common treatment for a baby with PKU. The child can be fed a special formula (Lofenalac) meant for babies with this condition. When the child starts eating solid food, phenylalanine must be avoided. It is common in NutraSweet/Aspartame, milk and eggs, among other foods.

Due to the restriction in the child's diet, a doctor may recommend certain supplements, such as fish oil, iron or carnitine. This is intended to support neurological development.

The dietary restrictions for babies with PKU must be strictly followed. If the diet is adhered to, the child can have a very good prognosis. However, if the diet and other treatments recommended by physicians are not followed, a child with PKU will have brain damage leading to mental retardation within the first year after birth.
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If you notice foul, musty smelling urine in an infant, it is best to seek a doctor's advice as soon as possible. Because smelly pee in babies could be a sign of a problem such as PKU, your child's symptoms should be evaluated by a professional.