Antimicrobial effectiveness of a nanosecond-pulsed dielectric barrier discharge (DBD) was investigated and compared with that of a microsecond-pulsed DBD. Experiments were conducted on the Escherichia coli bacteria covering a topographically non-uniform agar surface acting as one of the DBD electrodes. They reveal that the nanosecond-pulsed DBD can inactivate bacteria in recessed areas whereas the microsecond-pulsed and conventional DBDs fail to do so. Charged species (electrons and ions) appear to play the major role in the bacteria inactivation with the nanosecond-pulsed DBD. Moreover, the nanosecond-pulsed DBD kills bacteria significantly faster than its microsecond-pulsed counterpart. © 2009 IOP Publishing Ltd.