The aim of this study was to assess the effect of cigarette smoke inhalation (CSI) on gene expression in alveolar bone healing sites. Wistar rats were randomly assigned to the groups: control [animals not exposed to CSI (n = 20)] and test [animals exposed to CSI, starting 3 days before teeth extraction and maintained until killing them (n = 20)]. First mandibular molars were bilaterally extracted, and the expression of alkaline phosphatase, bone morphogenetic protein (BMP) 2 and 7, receptor activator of nuclear factor κB ligand, osteoprotegerin, and d2 isoform of vacuolar adenosine triphosphatase V(0) domain were assessed by quantitative polymerase chain reaction in the newly formed tissue in the sockets. Overall, data analysis demonstrated that CSI significantly affected the expression pattern of all of the studied genes except BMP-7. The expression of key genes for bone healing may be affected by CSI in tooth extraction sites.