Beckwith-Wiedemann syndrome affects 1 in 10,500 to 13,700 newborns worldwide. The condition may actually be more common than this estimate because some people with mild symptoms are never diagnosed.

The genetic causes of Beckwith-Wiedemann syndrome are complex. The condition usually results from the abnormal regulation of genes in a particular region of chromosome 11. People normally inherit one copy of this chromosome from each parent. For most genes on chromosome 11, both copies of the gene are expressed, or "turned on," in cells. For some genes, however, only the copy inherited from a person's father (the paternally inherited copy) is expressed. For other genes, only the copy inherited from a person's mother (the maternally inherited copy) is expressed. These parent-specific differences in gene expression are caused by a phenomenon called genomic imprinting. Abnormalities involving genes on chromosome 11 that undergo genomic imprinting are responsible for most cases of Beckwith-Wiedemann syndrome.

At least half of all cases result from changes in a process called methylation. Methylation is a chemical reaction that attaches small molecules called methyl groups to certain segments of DNA. In genes that undergo genomic imprinting, methylation is one way that a gene's parent of origin is marked during the formation of egg and sperm cells. Beckwith-Wiedemann syndrome is often associated with changes in regions of DNA on chromosome 11 called imprinting centers (ICs). ICs control the methylation of several genes that are involved in normal growth, including the CDKN1C, H19, IGF2, and KCNQ1OT1 genes. Abnormal methylation disrupts the regulation of these genes, which leads to overgrowth and the other characteristic features of Beckwith-Wiedemann syndrome.

About twenty percent of cases of Beckwith-Wiedemann syndrome are caused by a genetic change known as paternal uniparental disomy (UPD). Paternal UPD causes people to have two active copies of paternally inherited genes rather than one active copy from the father and one inactive copy from the mother. People with paternal UPD are also missing genes that are active only on the maternally inherited copy of the chromosome. In Beckwith-Wiedemann syndrome, paternal UPD usually occurs early in embryonic development and affects only some of the body's cells. This phenomenon is called mosaicism. Mosaic paternal UPD leads to an imbalance in active paternal and maternal genes on chromosome 11, which underlies the signs and symptoms of the disorder.

Less commonly, mutations in the CDKN1C gene cause Beckwith-Wiedemann syndrome. This gene provides instructions for making a protein that helps control growth before birth. Mutations in the CDKN1C gene prevent this protein from restraining growth, which leads to the abnormalities characteristic of Beckwith-Wiedemann syndrome.

About 1 percent of all people with Beckwith-Wiedemann syndrome have a chromosomal abnormality such as a rearrangement (translocation), abnormal copying (duplication), or loss (deletion) of genetic material from chromosome 11. Like the other genetic changes responsible for Beckwith-Wiedemann syndrome, these abnormalities disrupt the normal regulation of certain genes on this chromosome.