Background: Microbial penetration inside the implant’s internal hole creates a bacterial reservoir that is related with an area of inflamed connective tissue opposite the fixture-abutment junction and this can affect with the health of the peri-implant tissue. Chlorhexidine (CHX) has been used to prevent internal implant contamination as a 0.2% solution, a varnish or gel. Aim: To evaluate the aerobic/anaerobic bacterial count-reduction potential of 2% CHX gel placed, at the time of surgery, in the implant screw hole over a period of minimum 90 d, and to monitor the periodontal health status of all patients, throughout the study. Material and methods: Ten partially edentulous patients received 30 DI and these implants were randomly allocated in to: Group I (test) 15 implants applied by flap or flapless surgery with 2% CHX gel application. Group II (control) 15 implants applied by flap or flapless surgery without CHX gel application. All patients were examined clinically to determine their oral health status by examination of their plaque index, PLI, Gingival index GI, Bleeding on probing, BOP, and probing pocket depth, PPD, every two weeks throughout the study. Three months later, the plaque sample was collected from the internal hole of fixture and was sent for bacteriological examination. Results: The present study shows highly significant reduction of aerobic count of bacteria from 52.1% to 100%. Also, anaerobic bacterial count was reduced from 64.6% to 100% for group that received 2% CHX gel in screw hole of implants at time of surgery. When compared, the count of aerobic and anaerobic bacteria (CFU) between test and control group, a significant reduction was found. Conclusion: The use of 2% CHX gel at the time of placement can significantly reduce bacterial counts in the implant screw hole, and this effect can be maintained for 90 d or longer.