The cause of a cleft is still unknown, although recent research findings have found there to be a specific gene that increases threefold the occurrence of clefts.Some medications, when taken by the mother during pregnancy, have been linked to clefting. Smoking is another factor. Furthermore, recent studies have shown a link between clefts and environmental factors such as air pollution.
In our case, we don't really know why this has happened to BOTH of our children. I have met many parents who are in the same boat we are. We don't have family history, I have never smoked or drank in my life, and I have never taken medication while pregnant (other than prenatals). It may be forever a mystery to us. After meeting with a geneticist, we have been told that there is some sort of genetic trigger that is causing our children to have a predisposition to clefts.
I think that is one thing that makes dealing with a cleft so emotionally hard- is that there aren't a lot of answers right now as to why it occurs. I wish there were, but there just aren't. A mother naturally is inclined to blame herself for anything going wrong with a baby she has carried for the last 9 months, and I strongly advocate mothers to not burden themselves with this guilt. I blamed myself for 2 years after my first son Jimmy was born. I didn't understand the cleft and blamed myself for starting my prenatals too late into the pregnancy. It wasn't until our second son was diagnosed with a cleft via ultrasound (whom I had started taking prenatals with 3 months prior to conception), that I finally realized this wasn't about me doing something wrong, but something happening that was out of my control. I honestly wish I could take each new mommy by the shoulders and urge her over and over again to not blame herself for this. It's not your fault, and you did nothing to cause this.
Now, back to the basics. While the cleft anomaly can "run in families" or show in conjunction with syndromes (e.g., Pierre Robin Sequence, Crouzon Syndrome, Treacher Collins), most often a cleft shows itself as an "isolated incident". This means that, at first investigation, there is no family history and no indication of other health problems. This is also known as a nonsyndromic cleft. Both of my sons have been diagnosed as nonsyndromic.
When someone is born with a cleft, they can be born with a cleft of the LIP, the PALATE, or both. It is actually most common to be born with both the lip and palate affected.
When someone is born with a cleft LIP, they have an opening in the upper lip. Normally the lip is formed by the union of two tabs of tissue that grow in from the sides of the face with a central tab that grows down from the tip of the nose. This union takes place around 4-6 weeks of embryonic development. Here is an excellent picture of these fusion points:
When I was in the hospital, shortly after my first son was born, my brother Marcus (who was in Medical School at the time), gave me a wonderful explanation of how the cleft occurs. He told me that the formation of our face is actually quite complex. I remember he held his 2 hands together in a cupping shape and and proceeded to fold his fingers inward explaining that there are a number of tabs that fold inward and latch. These folds give rise to our nose and our mouth. Here is another picture depicting a 5 week fetuses (this is what we all looked like at 5 weeks old!) that shows the places where our lips latch very clearly:
Picture is from the book "A Child is Born" by Lennart Nilsson and Lars Hamberger 4th Ed., page 97. Caption reads: Now we can see the eyes, nose and mouth- a developing face. The nostrils have formed above the opening that will be the mouth, but the groove between the nostrils and the edge of the top lip has not yet been effaced... 30 days, 7 mm/0.26 in.
Another way to get a good idea of what I am talking about, is to take a look at your face in the mirror.
See those 2 small lines coming down from your nostrils to the tips of your cupid's bow of your lips? Those lines are called the philtrum and are "scars" from the folds where your face came together during embryonic development. This fusion should take place in the fourth to sixth week of pregnancy. If the union is not complete, the baby is born with a cleft lip. Now, there are different kinds of clefts that can occur with the lip. Both of my boys have differing clefts which I have always found to be interesting.If the cleft extends up into the nostril it is called a ‘complete cleft lip’.
If the nose is not affected it is called an ‘incomplete cleft lip’. 
When both sides of the lip don't latch, then it is a bilateral cleft lip.
When it is just one side that doesn't latch then it is called a unilateral cleft lip as depicted in the pictures above. With my boys' cases, they were each born with a unilateral cleft lip, but on opposite sides. So Jimmy's right lip decided not to latch, and Johnny's left lip. Also, Johnny was born with a complete cleft, while Jimmy's was incomplete.When a cleft of the palate occurs, it can affect the hard and soft palate. Here's a little way to explain where your hard and soft palate are. Open your mouth wide and look into a mirror. Place your tongue at the top of your mouth, near the front by your teeth. You will notice this is hard and is likewise your HARD palate. If you look at your hard palate in the mirror, you may even be able to see the whitish line down the center, where your palate "zippered shut" in the embryonic stage of development.
Now look further back in your mouth. Move your tongue from the hard roof of your mouth back towards where it becomes soft and elastic. This is where your soft palate begins. If you look far enough back, you will see your little uvula (the little ball which hangs down) and that is the end tip of the soft palate.
Like the lip, there are varying forms of a cleft of the palate. Some babies are born with just the soft palate affected by a cleft. Other babies are born with the entire roof of the mouth (both hard and soft palates) affected. For both of my boys, they had a cleft of the hard and soft palate and the uvula ball was split into two.
There are also very minor forms of clefts of the soft palates which include a submucosal cleft and a clefted uvula. I couldn't find a picture of a submucosal cleft, but I did find one of a clefted uvula:
