The etiology of denture stomatitis remains controversial. Trauma due to unstable dentures has been suggested as an etiological factor. Therefore, we tested the hypothesis that the prevalence of denture stomatitis is reduced when mandibular dentures are stabilized by implants. Data were collected at a one-year follow-up from 173 edentulous elders who had randomly received mandibular implant overdentures or conventional dentures. The diagnosis of denture stomatitis was determined according to the Newton classification. Elders wearing conventional dentures were almost 5 times more likely to have denture stomatitis than those wearing mandibular two-implant overdentures (P < 0.0001, Fisher's exact test). Adjusted odds ratios showed that only the type of the prosthesis (AOR = 4.54, 95% CI 2.20 to 9.40) and nocturnal wear (AOR = 3.03, 95% CI 1.24 to 7.40) predict the frequency of denture stomatitis. Thus, implant overdentures may reduce oral mucosal trauma and control denture stomatitis.