Since the advent of osseointegration some 50-years ago, oral implants have been placed in an alveolar bone bed of presumed sterility (intraradicular infection theory). Bacteria were excluded from the pathogenesis of dental implant failure. Clinical audit of fixture failure provided an association with previous tooth-borne infection and soft bone. Extraradicular infection theory provided evidence for bacterial persistence in alveolar bone. A study was designed to test the hypothesis that apparently sterile alveolar bone may harbour a nidus of residual biofilm bacteria which is refractory to non-surgical treatment. A possible commensal biofilm within alveolar bone raised the issue of a resident homeostatic microbiota optimising osseointegration by sustaining an ecologically stable state. Here we show that culture microbiology revealed the presence of bacteria in 21% of apparently healed alveolar bone ridges. Scanning electron microscopy (SEM) visually confirmed the bacterial presence as biofilm. The use of 454-pyrosequencing in analysing 153 clinical samples from 40 patients revealed that no sterile sites were found in bone beds for implants. Polymicrobial assemblages were also revealed in two “health” control sites of congenital tooth absence. Clinical audits revealed that a statistically significant effect existed between debridement and fixture success. The association of debridement beyond the sclerosis with implant outcome (success/failure) revealed a small to medium effect size (w=0.2) with a clinical power of 96% and p<0.001. The results seem to indicate that intraradicular infection theory is no longer valid. It would seem that an extraradicular polymicrobial biofilm exists with an almost infinite number of alternative stable states. Surgical debridement beyond sclerosis may be instrumental in improving osseointegration outcomes. There is limited but interesting evidence for the existence of a commensal biofilm in alveolar bone.