The incidence of fluoroquinolone-resistant (FQR) Haemophilus influenzae and Moraxella catarrhalis isolated from clinical specimens remains very rare, and the identification of such strains has been previously limited to case reports from diverse geographic locations. During the 1997 through 1998 SENTRY Antimicrobial Surveillance Program, four FQR-H. influenzae (0.13% of all strains) and one FQR-M. catarrhalis strains were identified and confirmed as having elevated MICs to > or =5 FQ class drugs. Among H. influenzae strains, MICs to marketed FQs were > or =0.12 microg/ml with ciprofloxacin MIC results > or =8-fold higher than wild type susceptible strains. The FQR-H. influenzae isolates were then compared with two previously reported strains that were determined to be identical using ribotyping and other molecular methods. In contrast, the SENTRY isolates were all genetically distinct and had mutations in parC and/or gyrA. Isolates having the lowest MIC elevations had a single mutation in gyrA, while isolates with higher MICs had at least one mutation in both studied genes. In general, the single gyr A mutations involved the same position but differed in the amino acid substitution (Ser84Leu or Phe or Ala). The isolates reported outside the SENTRY Program (controls) had an unusual mutation in par C (Gly82Asp) and two mutations in gyr A; producing the highest recorded FQR MICs. The FQR-M. catarrhalis strain was discovered in late 1997 and has been reported before. Although detection of these FQR isolates remains at <1% of all contemporary H. influenzae and M. catarrhalis isolates, surveillance programs will be an important detection method to determine the extent of emerging novel resistance patterns among clinically prevalent fastidious pathogens.