What Causes a Cleft Lip and Alveolus During Pregnancy?

It is incredibly common for parents to wonder if they did something wrong to cause their baby’s cleft lip and alveolus, but the answer is a definitive no. An isolated cleft lip and alveolus—meaning the cleft is the only condition present and not part of a broader genetic syndrome—is caused by a complex, largely unpredictable combination of genetic and environmental factors that interact very early in the first trimester ^[1][2]. Normal daily activities—like having a cup of coffee, experiencing a minor bump to your stomach, or continuing to work—do not cause a cleft lip ^[3][4][5]. The development of the baby’s face happens so early in pregnancy that the lips and gums are often actively forming before a woman even realizes she is pregnant.

How and When the Cleft Forms

The upper lip and the alveolus (the gum ridge that holds the teeth) begin to form between the 4th and 7th weeks of pregnancy ^[6][7]. It is completely normal and very common to not even know you are pregnant during this time. During this narrow window, tissues from opposite sides of the baby’s developing face grow toward each other to connect.

A cleft lip and alveolus occurs when the medial nasal processes and maxillary processes (the specific structures that form the center and sides of the upper face) fail to fuse completely ^[6][7][8]. Because the formation of the primary palate (which includes the lip and alveolus) is completed by the end of the second month of pregnancy, nothing you did later in your pregnancy could have affected or changed this outcome ^[9][10].

A “Multifactorial” Condition

Doctors describe the cause of most isolated clefts as multifactorial, meaning it takes a specific combination of several different factors lining up in exactly the wrong way to cause the cleft ^[3][4][5]. It is almost never the result of a single event or action.

• Genetic Factors: Genes act as the instruction manual for the baby’s development. Research has identified multiple genes (such as IRF6, MSX1, and SATB2) that help coordinate the delicate process of facial fusion ^[11][12]. Sometimes variations in these genes are passed down through families, but often they occur completely randomly ^[13].
• Environmental Triggers: Genetics do not operate in a vacuum; they interact with the mother’s body in complex ways ^[1]. Certain high-risk exposures—such as specific anti-seizure medications, taking certain opioid medications, smoking or tobacco use, alcohol consumption, or a lack of folic acid very early in pregnancy—have been linked to a higher chance of clefts ^[14][15][16]. (Note: If you are taking prescribed medications, never abruptly stop them without consulting your doctor. Furthermore, many women who take prenatal vitamins perfectly still have babies with clefts, as vitamins are just one small factor among many).

Releasing the Guilt: What Does NOT Cause a Cleft

Mothers often spend hours retracing their steps during early pregnancy, looking for something to blame. It is vital to understand that the medical evidence shows everyday events and activities do not cause clefts ^[3].

• Normal stress or working: Occupational stress or a busy, active lifestyle does not disrupt facial fusion ^[3].
• A bump to the belly: The baby is highly protected in the uterus by amniotic fluid. Minor physical trauma, falls, or bumps do not cause the lip or gums to separate ^[3][5].
• Having a cup of coffee: While health authorities suggest limiting overall caffeine during pregnancy for general health, normal coffee consumption does not single-handedly cause a cleft lip and alveolus ^[3][4].

Even if you did everything perfectly—took all your vitamins, avoided all known risks, and rested flawlessly—a cleft can still happen simply due to unpredictable, microscopic genetic events ^[1][2]. You did not cause this.

What to Expect Next

Now that you know you did not cause this, you can focus your energy on preparing for your baby’s arrival. Your next step will likely involve meeting with a specialized cleft and craniofacial team. These multidisciplinary teams include specialized surgeons, orthodontists, and feeding specialists who will outline exactly how your baby’s lip and alveolus will be repaired ^[17][18]. If you are concerned about the risks for future pregnancies, you may also choose to speak with a genetic counselor.