In the present study we evaluated the efficacy of various procedures recommended for the disinfection of respiratory equipment and other materials in cystic fibrosis, using both planktonic and sessile Burkholderia cenocepacia cells. A modified European Suspension Test was performed to determine the effects of the disinfection procedures on planktonic cells. The ability of the treatments to kill sessile cells and to remove biofilm biomass was evaluated using two resazurin-based viability assays and a crystal violet staining on biofilms grown and treated in 96-well microtitre plates. The effect of chlorhexidine and hydrogen peroxide treatments on the viability of sessile B. cenocepacia cells was clearly reduced compared to the effects on planktonic cells. Treatments with low concentrations of sodium hypochlorite (0.05%, 5 min) and acetic acid (1.25%, 15 min) also resulted in insufficient reductions in the number of viable sessile cells. There was no relation between the ability of the disinfectants to remove biofilm biomass and their potential to kill biofilm cells. In conclusion, our study indicates that testing of the efficacy of disinfectants should be performed on both planktonic and sessile cells, with particular attention to their effects on cellular viability.