Congenital abnormalities are worldwide major health problem. One of these abnormalities is; cleft lip and palate. Such a condition when occur, it can affect the child and provoke physiological and psychological consequences. One of the desired and sparkling line of treatment is stem cells engineering. There are many different types of stem cells. The most popular stem cells used in craniofacial treatment are; bone marrow derived mesenchymal stem cells (BM-MSCs) and adipose tissue derived mesenchymal stem cells (AT-MSCs). Although both showed positive results, still there are few comparative studies that evaluate the effectiveness of AT-MSCs over BM-MSCs. The purpose of this review was to provide an overview of stem cells and their clinical uses, and to compare the effectiveness of BM-MSCs and AT-MSCs in cleft lip and alveolus patients. Electronic search of English scientific papers from 2000 to 2017 was accomplished using PubMed, Cochrane Database and Google Scholar search engines. The following search terms used were, Cleft Lip and Palate, Bone Marrow Derived Mesenchymal Stem Cells, Adipose Tissue Derived Mesenchymal Stem Cells, Clinical Applications in Dentistry, Animal Studies. Stem cells offer a new era for craniofacial reconstruction. Both of adipose and bone marrow derived stem cells show effective results in the level of restoring function and esthetic. However, the AT-MSCs were easier to obtain without any harm to the patients.