Sixty days of ciprofloxacin administration at 500 mg every 12 h is currently recommended for the prophylaxis of inhalational exposure to Bacillus anthracis. We examined Bacillus anthracis (Delta-Sterne strain) in our hollow-fiber infection model. We measured the ciprofloxacin concentrations achieved and the number of organisms present before heat shock (total population) and after heat shock (spore population). We fit a mathematical model to these data. Monte Carlo simulation with differing initial spore burdens (3, 5, and 6.9 log(10) CFU/ml) demonstrated that 35 days of this regimen would completely clear the spore burden in 95% of patients. Durations of 110 days did not achieve 99.9% eradication, irrespective of initial burden, because of between-patient variance in drug pharmacokinetics. Given the absence of person-to-person transmission for Bacillus anthracis, adverse drug effects with long-term ciprofloxacin administration, and the possibility of engendering resistance in bodily flora, shorter prophylaxis duration should be given consideration, along with careful monitoring of all exposed individuals.