GERD is a common condition and acid-suppressing agents are the mainstay of treatment. A cost-effectiveness analysis comparing a PPI, lansoprazole (LPZ) and a H2RA, famotidine (FAM) for the maintenance treatment of reflux esophagitis in Japan was performed using a Markov chain approach. The time period studied was 6 months and payer perspective was chosen. Transition probabilities were estimated from meta-analyses. Expected days without esophagitis (healthy days) were 166 for LPZ 30 mg/day, 161 for LPZ 15 mg/day and 143 for FAM 40 mg/day. Direct costs were 55,624 yen for LPZ 30 mg/day, 42,078 yen for LPZ 15 mg/day and 67,969 yen for FAM 40 mg/day. Cost-effectiveness ratio (direct costs/healthy days) was 335 yen for LPZ 30 mg/day, 262 yen for LPZ 15 mg/day and 477 yen for FAM 40 mg/day. Lansoprazole was superior to famotidine with regard to both efficacy and cost-effectiveness and therefore is the preferred therapeutic agent for the maintenance treatment of GERD.