Some antibiotic solutions increase bacterial resistance and may cause toxic side effects. Heparin, frequently used as an anticoagulant in catheter lock solutions, may cause bleeding and stimulate biofilm formation. The aim of this study was to investigate the effect of a new antibacterial/antithrombotic solution, citrate/Methylene Blue/parabens (C/MB/P), versus various heparin solutions on the viability and the structure of preformed mature biofilms of Staphylococcus aureus bacteria. The degree of eradication of both planktonic and sessile microorganisms was evaluated. The changes in the structure of biofilms after exposure to C/MB/P and several concentrations of heparin were analysed by means of confocal laser scanning microscopy. COMSTAT image analysis was utilized to compare biofilm biomass, average and maximum height, surface coverage and roughness coefficient. Viability studies were performed on both biofilms and supernatant solutions. C/MB/P, in contrast to heparin solutions, significantly reduced biofilm biomass and thickness and reduced viability by 5 log when compared with saline treatment. No viable planktonic bacteria were detected and the few remaining biofilm cells appeared to be lysed. In contrast, most heparin solutions only reduced viability up to 1.0 log and failed to eradicate planktonic bacteria. C/MB/P has a rapid bactericidal effect on the preformed, mature biofilm of S. aureus. The structural changes of biofilms treated with C/MB/P, together with the observed log reduction of viable biofilm cells, confirmed the high potential of this solution to eliminate sessile bacteria. Furthermore, the tested solution entirely eliminated planktonic bacteria detached from the biofilm.