:I feel that I have to make a comment here (I stated in an earlier post to find it 'offensive'). First let me explain why I made that comment in the first place. At the time I made the comment, the article looked like it stressed the drug/alcohol factors too much. Basically the drug/alcohol factors were stated at the same level as genetic factors. To me (at the time), it looked as if the article told readers to think "he there is a kid with cleft, their parents must be either drunk or drug addicts". (I will not deny that it is possible that personal emotion (3 family members with cleft) influenced this line of thought). 
 :Now, cleft is indeed multi-factoral, and yes, alcohol and drugs are factors. However, this can be said for nearly any deformity formed during pregnancy. Drugs and alcohol are bad for pregnancies in general. The genetic specialists in our craniofacial team has been participating in a large scale research (cooperation between several dutch and german hospitals with cleft treatment teams) told me that the research confirmed that smoking increased the odds from 0.3% to  ~0.8%, while having one family member increases the odds from 0.3% to 7%-10%. So yes, smoking is a factor but it is not as significant as the genetics. The reason while it is "muti-factoral" is because one can have a child with cleft while there is no genetic cause apparent. Therefore other factors must be in play. Unfortunately I can't find the research published on the Internet so it is hard to cite this source. I will ask next time I am at the hospital (which is probably soon, my youngest son's lip will be closed within a few weeks).