The development of the craniomandibular system is guided by genetic interactions and environmental factors, including specific habits such as breastfeeding, bottle feeding, thumb sucking and the use of pacifiers. These habits can have a considerable impact on the growth of the developing jaws and can lead to malocclusion in children. This review aims to investigate potential associations between non-nutritive sucking habits (NNSHs) and malocclusions compared to the presence of nutritive sucking habits (NSHs). To carry out this systematic review, we followed the PRISMA protocol and performed a bibliographic search of the existing literature until April 2023 in the following electronic databases: Medline, PubMed, The Cochrane Library and Embase. Out of a total of 153 records, we included 21 studies. We found that the chances of diagnosing a malocclusion were higher for children with bottle nutrition when compared to breast-fed children. Breastfeeding provides protection against malocclusions. In the same manner, persistent NNSH habits appeared to be associated with increased chances of having malocclusions. The longer the child was breastfed, the shorter the duration of the pacifier habit and the lower the risk of developing moderate/severe malocclusions. The duration of the habits has a positive influence on the appearance of occlusion defects.