Glass ionomer cements have been suggested for obturating carious teeth that have been prepared with dental hand instruments. In such cases, carious dentine may be inadvertently or deliberately left in situ. The residual bacteria may, over time, lead to secondary caries and restoration failure. Benefit may be gained from combining antibacterial agents with the glass ionomer cement to control residual bacteria. The aim of this study was to investigate the effects on the compressive strength of glass ionomer cement combined with oral antibacterial agents. Cationic antibacterial agents; chlorhexidine hydrochloride, cetylpyridinium chloride and cetrimide were added to the powder and benzalkonium chloride, a liquid, to the liquid of Fuji IX glass ionomer cement. These were prepared to concentrations of 1, 2 and 4 per cent by weight of the glass ionomer cement and compared to Fuji IX with no antibacterial agent. Test specimens were subjected to a compressive force to failure. Multiple analysis of variance showed highly significant reductions in compressive strength (p < 0.01) between the test materials and control group apart from one per cent benzalkonium chloride. Increasing concentration of the antibacterial agent had increasing adverse effects on the physical properties. The addition of the antibacterial agents tested to Fuji IX reduces the seven-day compressive strength which may affect the clinical performance of the material.