The use of Nd:YAG laser for bacterial reduction as an adjuvant to non-surgical periodontal treatment has been approached in several studies. Furcation complex anatomy is responsible for comprised treatment results in this areas due to the lack of proper access for instrumentation showing the persistence of a pathogenic microbial flora. The purpose of this clinical trial, randomized, double-blinded was to evaluated the bacterial reduction achieved with the Nd:YAG laser associated to conventional treatment on furcation sites of 17 patients with chronic periodontitis. They received previous full mouth periodontal treatment except for the experimental sites. In a split mouth design study, 34 class 11 furcations were selected and divided in two groups. The 17 furcations of the control group underwent twice manual and ultrasonic root debridment in weekly intervals. The test group received the same treatment as the control group followed by the Nd:YAG laser application (100 mJ/pulse, 1.5 W, 15 Hz, 60 see.). The microbiological parameters - total number of anaerobic Colony Forming Units (CFU), Black pigmented CFU and the level of A. actinomycetemcomitans, P. gingivalis and P. intermedia - were determined at baseline. immediately and one month after the treatment. The results showed a significant reduction of total CFU for both groups immediately after treatment, but it was better for the test group. After one month the total CFU average increased but was still below pretreatment levels for both groups. The Black pigmented CFU and the level of A. actinomycetemcomitans. P. gingivalis and P. intermedia decreased significantly after the treatment but 30 days after. there was an increase almost equal to baseline levels for both groups. The Nd:YAG laser associated with conventional treatment promoted bacterial reduction on class II furcation immediately after its application.