This trial will follow an adaptive trial design, whereby information regarding PerioSept(r) drug levels will be obtained via a PK trial lead in period (PK Pilot) in a limited number of subjects (up to N=8). This will be followed by the main safety and efficacy trial of PerioSept(r) as an adjunct to scaling and root planing (SRP) in subjects with moderate to severe periodontitis (Main Trial, N=87). The PK Pilot will be an open label PK study. Up to 8 qualifying subjects will receive SRP on Day 1 followed by 3% PerioSept(r) administered in a minimum of 4 qualifying periodontal Study Pockets in at least 2 quadrants with a probing pocket depth (PPD) ≥ 5mm and bleeding on probing (BOP) and at least 20 other qualifying pockets (PPD ≥ 5 mm). The Main Trial will be a multi-center, randomized, blinded, placebo controlled, parallel arm trial of PerioSept(r) (0.3%, 1% or 3%) administered up to three times (over Days 1 and 2, at Weeks 4 and 12) into a minimum of 4 qualifying periodontal Study Pockets in at least 2 quadrants with a PPD ≥ 5mm and BOP following SRP at baseline. All other eligible pockets with a PPD ≥ 5mm will also be treated.