Aim: Comparing the bacterial adherence and count on denture bases and underlying mucosa when using chrome-cobalt Co-Cr (Metal), Acetal and Polyether ether keton (PEEK) as denture base materials. Materials and Methods: 20 patients with mandibular Kennedy class III Mod. 1, opposing maxillary fully dentulous ridge were selected. Patients were divided into two groups 10 each. Group I: In a split mouth, patients received removable partial denture with chrome cobalt (Metal) denture base on one side and Acetal denture base on the other side. Group II: In a split mouth patients received chrome cobalt (Metal) denture base on one side and PEEK denture base on the other side. Swabs were taken from the fitting surface of dentures and the mucosa underlying the denture at 1 week, 2 weeks and 3 weeks after insertion. Incubation on blood agar for 24 hours at 37 degrees was done. Results: On the denture base: Acetal showed 6.93±0.08, Metal 6.48±0.15, and Peek 6.85±0.17. On the mucosa: Acetal showed 6.52±0.13, Metal 6.51±0.18, and PEEK 6.55± 0.12. There was insignificant difference between the Acetal and Peek, however metal showed significant difference when compared with other materials. Conclusion: The bacterial count was low on the mucosal surface for the three materials. For the fitting surface both PEEK and acetal resin showed higher count compared to the metallic denture base through the follow up period.