Ketone compounds that are widely used in various manufacturing processes are known as high-priority toxic volatile organic compounds (VOCs). The use of biofiltration systems for the removal of VOCs from a polluted air stream has attention because of the inherent advantages of these systems such as high removal efficiency and low installation and maintenance costs. In this study, a biofiltration system for the removal of ketone compounds (acetone, methyl ethyl ketone (MEK)) was developed using laboratory scale three-layer biofilter beds packed with ceramic-type media (bed volume 5 L). The operating conditions were optimized on the basis of environmental parameters, and mixed cultures of microorganisms obtained from a sewage treatment plant were inoculated to induce microbial biofilm formation. This system was operated at an empty bed retention time (EBRT) of 15-30 s under nitrogen-deficient conditions, and 1 L of the nutrient solution was supplied every two weeks. During the operation time of approximately three months, the removal efficiency was found to be more than 97% at when the inlet acetone concentration was 110-720 ppm(v) and 90% when the inlet MEK concentration was 91-591 ppm(v). These removal efficiencies corresponded to removal capacities of 31-93 gm(-3) h(-1) and 16-85 gm(-3) h(-1), respectively. The maximum elimination capacity for acetone and MEK was approaching to 300 gm(-3) h(-1) and 200 gm(-3) h(-1), respectively. By using GC/MS analysis, methanol was detected in the outlet stream when the biofilter was used for acetone removal, and methanol and acetone were detected in the outlet stream when the biofilter was used for MEK removal.