We attempted to determine the economic impact of three alternatives for the treatment of chlamydial infections in the emergency department: a written prescription for 7 days of doxycycline therapy (D-RX); a prepacked 7-day supply of doxycycline (D-ED); or a single 1-g dose of azithromycin (AZI). Data inputs for the model were obtained from both patient experience and literature sources. Primary health outcomes of the model were number of infection relapses. Economic outcomes were costs for initial treatment, treatment of relapses, and treatment of complications of relapse. For every 1000 patients, D-ED and AZI resulted in 21.6 (-10 to -41) and 36.2 (-25 to -63) fewer relapses than D-RX, respectively; AZI resulted in 14.6 (-35 to -4) fewer relapses than D-ED. Total costs were decreased for D-ED and AZI versus D-RX by $18,879 (-$39,000 to -$8000) and $24,039 (-$59,000 to -$10,000), respectively, and AZI resulted in a total cost decrease of $5160 (-$35,000 to +$6000) versus D-ED. Both D-ER and AZI decreased infection relapses and overall health care costs compared with D-RX. Also, AZI resulted in additional decreases in relapses versus D-ED, although the incremental impact on cost was inconclusive.