Individuals with Down syndrome have a higher risk for many conditions. The medical consequences of the extra genetic material in Down syndrome are highly variable and may affect the function of any organ system or bodily process. 

Some problems are present at birth, such as certain heart malformations. Others become apparent over time, such as epilepsy.

Congenital heart disease

The incidence of congenital heart disease in children with Down syndrome is up to 50%. 

A atrioventricular septal defect also known as endocardial cushion defect is the most common form with up to 40% of patients affected. This is closely followed by ventricular septal defect that affects approximately 30% of patients.

Malignancies

Hematologic malignancies such as leukemia are more common in children with DS. In particular, the risk for acute lymphoblastic leukemia is at least 10 times more common in DS and for the megakaryoblastic form of acute myelogenous leukemia is at least 50 times more common in DS. 

Transient leukemia is a form of leukemia which is rare in individuals without DS but affects up to 20 percent of newborns with DS. This form of leukemia is typically benign and resolves on its own over several months, though it can lead to other serious illnesses. 

In contrast to hematologic malignancies, solid tumor malignancies are less common in DS, possibly due to increased numbers of tumor suppressor genes contained in the extra genetic material.

Thyroid disorders

Individuals with DS are at increased risk for dysfunction of the thyroid gland, an organ which helps control metabolism. Low thyroid (hypothyroidism) is most common, occurring in almost a third of those with DS. This can be due to absence of the thyroid at birth (congenital hypothyroidism) or due to attack on the thyroid by the immune system. 

Reproduction is also affected by DS.

Gastrointestinal

Down syndrome increases the risk of Hirschsprung's disease, in which the nerve cells that control the function of parts of the colon are not present. This results in severeconstipation. 

Other congenital anomalies occurring more frequently in DS include duodenal atresia, annular pancreas, and imperforate anus. Gastroesophageal reflux disease and celiac disease are also more common among people with DS.

Infertility

There is infertility amongst both males and females with Down syndrome; males are usually unable to father children, while females demonstrate significantly lower rates of conception relative to unaffected individuals. 

Women with DS are less fertile and often have difficulties with miscarriage, premature birth, and difficult labor. Without preimplantation genetic diagnosis, approximately half of the offspring of someone with Down syndrome also have the syndrome themselves. 

Men with DS are almost uniformly infertile, exhibiting defects in spermatogenesis. There have been only three recorded instances of males with Down syndrome fathering children.

Neurology

Children and adults with DS are at increased risk for developing epilepsy. The risk forAlzheimer's disease is increased in individuals with DS, with 10-25% of individuals with DS showing signs of AD before age 50, up to 50% with clinical symptoms in the sixth decade, and up to 75% in the 7th decade. This sharp increase in the incidence and prevalence of dementia may be one of the factors driving the decreased life expectancyof persons with Down Syndrome.

Ophthalmology and otolaryngology

Eye disorders are more common in people with DS. Almost half have strabismus, in which the two eyes do not move in tandem. Refractive errors requiring glasses or contacts are also common. 

Cataracts (opacity of the lens) and glaucoma (increased eye pressures) are also more common in DS. Brushfield spots (small white or grayish/brown spots on the periphery of the iris) may be present.

Other complications

In the past, prior to current treatment, there was a 38-78% incidence of hearing loss in children with Down syndrome. Fortunately, with aggressive, meticulous and compulsive diagnosis and treatment of chronic ear disease (e.g. otitis media, also known as Glue-ear) in children with Down syndrome, approximately 98% of the children have normal hearing levels.

Instability of the atlanto-axial joint occurs in ~15% of people with DS, probably due to ligamental laxity. It may lead to the neurologic symptoms of spinal cord compression. Periodic screening, with cervical x-rays, is recommended to identify this condition.

Other serious illnesses include immune deficiencies.

These factors can contribute to a shorter life expectancy for people with Down syndrome. One study, carried out in the United States in 2002, showed an average lifespan of 49 years, with considerable variations between different ethnic and socio-economic groups. However, in recent decades, the life expectancy among persons with Down syndrome has increased significantly up from 25 years in 1980. 

The causes of death have also changed, with chronic neurodegenerative diseasesbecoming more common as the population ages. Most people with Down Syndrome who live into their 40s and 50s begin to suffer from an Alzheimer's disease-like dementia.