Photodynamic therapy (PDT) offers potential as a non-invasive treatment of periodontal disease. In this study, microcosm biofilms were grown in vitro under conditions designed to mimic subgingival plaques typically found in patients with periodontitis. To investigate potential PDT modalities, biofilms were exposed to light from a helium/neon laser in conjunction with a photosensitizer, toluidine blue O (TBO), at varying output and concentration, respectively. To determine cytotoxic effects, viability profiling was undertaken on whole biofilms using standard plating methods, and on horizontal cross-sections of biofilms using confocal laser-scanning microscopy (CLSM) in conjunction with a differential viability stain. A light energy dose of 94.5 J in combination with 81.7 μM TBO was found to be optimal, achieving significant kills of over 97%. CLSM enabled visualization of the effects of PDT in three dimensions. Viability profiling of the CLSM images revealed that lethal photosensitization was most effective in the upper layers of biofilm. PDT was found to reduce the viability of subgingivally modelled plaques in vitro by a magnitude similar to that of chlorhexidine digluconate, which is commonly used to treat periodontal disease. The findings of this study indicate that PDT may be an effective alternative to conventional modalities in the treatment of periodontal disease.