A cleft palate is usually caused by a mix of genetic and environmental factors that affect how a baby’s mouth forms in early pregnancy. In many individual cases, the exact cause is never fully known, but doctors do know a number of risk factors that make it more likely.

What a cleft palate is

  • A cleft palate is a gap or opening in the roof of the mouth that is present at birth.
  • It happens when the tissues that should fuse to form the hard and/or soft palate do not fully join between about weeks 6–12 of pregnancy.

Genetic causes

  • Many cleft palates are multifactorial , meaning several genes plus non-genetic factors are involved.
  • Sometimes a cleft palate is part of a broader genetic syndrome (for example, certain chromosomal or single‑gene conditions), and in 20–50% of cases genetics are considered a major contributor.

Environmental and pregnancy factors

Research has linked several maternal factors to a higher risk, though these do not guarantee a cleft will occur.

  • Smoking or alcohol use during pregnancy.
  • Certain medicines in early pregnancy, especially some anti‑seizure/anticonvulsant drugs and retinoid (vitamin A–related) drugs.
  • Poor folic acid intake and some nutritional deficiencies.
  • Maternal obesity and conditions that reduce oxygen to the embryo (hypoxia) have also been investigated.

Other possible influences

  • Exposure to substances such as pesticides, nitrates, organic solvents, and heavy metals like lead has been studied as possible contributors.
  • Use of certain illicit drugs (for example, cocaine) during pregnancy may increase risk in some studies.

Family history and chance

  • Having one child or close relative with a cleft lip/palate slightly increases the chance in a future pregnancy, because some susceptibility genes can run in families.
  • Even with a family history or risk factors present, many babies are born without clefts, and many clefts occur in families with no previous cases at all.

TL;DR: A cleft palate forms when the roof of the mouth does not close properly in early pregnancy, usually because of a combination of inherited genes and environmental or pregnancy‑related factors such as smoking, certain medications, or low folic acid, although in many babies the precise cause cannot be pinpointed.

Information gathered from public forums or data available on the internet and portrayed here.