This paper reports on the results of a structured review of the literature concerning in vivo molecular assessment of osseointegrated endosseous dental implants. A search of electronic databases was performed up to and including August 2011. Thirty articles met the inclusion criteria. A descriptive evaluation and analysis of the gene expression data concerning the process of osseointegration were performed. Broad consensus was observed among the study results, perhaps as a result of the similar targeted gene expression events. More recent investigations using gene arrays or gene profiling techniques offer new insights into the fundamental molecular events that support the osseointegration process. Evidence for the influence of surface topography on osteogenesis and osteoinduction has been reported. Additional investigations are required to further solidify the functional associations between individual or orchestrated gene expression events and the clinical result of osseointegration.