Neuraminidase (NA) inhibitors (NI) have recently been licensed for the prophylaxis and treatment of influenza virus infection in humans. This study has utilized a new chemiluminescent (CL) neuraminidase assay to routinely monitor more than a thousand influenza field isolates collected worldwide during the 2000-2002 seasons for susceptibility to both licensed NIs, zanamivir, and oseltamivir by determining the 50% inhibitory concentration (IC50). Our data demonstrated that influenza A viruses of the N2 subtype were less susceptible to zanamivir, but not oseltamivir, than those of the N1 subtype such that 41 of 45 confirmed H1N2 isolates could be reliably differentiated from H1N1 viruses based on their zanamivir susceptibility. Pre-titration of influenza A viruses appeared to have no effect on IC50 determined for either NI, while pre-titration of influenza B viruses significantly reduced oseltamivir IC50 and increased zanamivir IC50. Influenza B viruses were less susceptible to either compound than type A isolates. The CL assay is a rapid and reliable method for screening large numbers of influenza isolates for NI susceptibility. Reassortant viruses of the H1N2 subtype that started to circulate worldwide during the 2001-2002 season can be reliably separated from H1N1 viruses based on their zanamivir susceptibility, enabling large scale screening of H1 isolates for determining the prevalence of such reassortants.