Fanconi's syndrome is an impairment in proximal tubular function of the kidney. This impairment causes certain compounds, which should be absorbed back into the bloodstream by the kidneys, to be excreted in the urine instead.

Some compounds that may be lost in the urine include glucose, amino acids, uric acid, and phosphate. Loss of these compounds can cause problems, such as growth failure, decreased bone mineralization (rickets), and abnormal bone mineralization (osteomalacia).

Type two renal tubular acidosis (RTA) occurs when too much bicarbonate is excreted in the urine, causing excess acid in the blood (acidosis). Another problem that may result is dehydration caused by excess urination.

Fanconi's syndrome can be genetic or acquired later in life. Common causes of Fanconi's syndrome in children are genetic defects impairing the body's ability to break down certain compounds, such as the amino acid cystine (Cystinosis), fructose (fructose intolerance), galactose (galactosemia), and glycogen (glycogen storage diseases). Cystinosis is the most common cause of Fanconi's syndrome in children.

Lowe's disease (oculocerebrorenal syndrome), a rare genetic disorder of the eyes, brain, and kidneys, can also cause Fanconi's syndrome. Another genetic defect that can cause Fanconi's syndrome is Wilson's disease, which causes copper to collect in the kidneys, liver, eyes, and other organs. Similarly, exposure to heavy metals, such as lead poisoning, can cause Fanconi's syndrome, even when there is no genetic disease.

In adults, Fanconi's syndrome can be caused by various acquired disorders that damage the tubules of the kidneys. As in children, this damage can be caused by exposure to heavy metals such as lead, mercury, and cadmium.

The kidneys can also be damaged by prescribed drugs such as cidofovir (used to treat AIDS-related cytomegalovirus disease), gentamicin, tetracycline used after its expiration date, and azathioprine (used to suppress the immune system after organ transplantation, or to treat certain autoimmune disorders).

Kidney damage leading to Fanconi's syndrome can also be caused by dysproteinemias, diseases in which there are abnormal protein deposits in the kidney. These include multiple myeloma, light chain deposition disease, and primary amyloidosis. It can also occur as a result of a kidney transplant. Sometimes, in both children and adults, the cause of Fanconi's syndrome is not known.