The chromosomal multiple antibiotic resistance operon, mar, is widely represented amongst Gram-negative bacteria and has been implicated in resistance towards oxidative stress agents, organic solvents and a large number of structurally unrelated antimicrobial agents. The major mechanism associated with such increased resistance is an upregulation of the efflux pump acrAB. Growth as a biofilm is often associated with similar generalized reductions in susceptibility to inimical agents. Escherichia coli K12 (AG100), an isogenic mutant of AG100 constitutive for mar expression (AG102) and an isolate deleted of the mar locus (MCH164) were grown as biofilms in cellulose-fibre depth filters and perfused with a simple salts, minimal medium (CDM) over 120 h. Biofilms were exposed to various concentrations of ciprofloxacin (0.004, 0.015 and 0.1 mg/L) for 42 h. The numbers of viable cells within the perfusate and within the biofilm were estimated throughout. Whereas no differences were seen between the wild-type and mar-deleted isolates, that constitutive for mar displayed reduced susceptibility to ciprofloxacin at concentrations of 0.004 mg/L (MIC for AG100 was 0.0052 mg/L). Similar antibiotic perfusion experiments were conducted using isolates in which the efflux pump acrAB was either deleted (AG100-A) or constitutively expressed (AG100-B). Exposure of AG100-A biofilms to ciprofloxacin at 0.004 and 0.1 mg/L showed similar susceptibilities to those seen in the wild-type (AG100) and mar-deleted (MCH164) isolates and suggested that acrAB was not induced within the attached population. On the other hand, constitutive expression of acrAB (AG100-B) protected biofilms against the lower concentration of ciprofloxacin used (0.004 mg/L). This protection was again lost at concentrations of 0.1 mg/L. Overall, these results show that ciprofloxacin resistance in biofilms is not mediated by the upregulation of the mar or acrAB operons.