The aim of this study was to determine the interaction between omeprazole and amoxicillin, being common agents used in the eradication regimen for H. pylori infection. Amoxicillin concentrations in gastric mucosa and serum were quantitatively analysed in 12 patients with non-ulcer dyspepsia following the administration of one week duration of placebo as group I and omeprazole as group II. The study was a blind, cross-over design with a one week wash out period between the two treatment groups. Six antral gastric mucosa were biopsied 90 minutes after oral administration of amoxicillin. Blood samples were collected before and after administration at intervals up to 6 hours. All samples were analysed for amoxicillin concentration using the HPLC technique. Highly intersubject variations of amoxicillin concentrations were observed. The concentration of amoxicillin in gastric mucosa ranged from 0.00-1.74 and 0.00-1.25 micrograms/mg for group I and group II, respectively, with the mean concentration of 0.25 +/- 0.48 microgram/mg for group I and 0.28 +/- 0.40 microgram/mg for group II. The difference was not statistically significant (p = 0.89). Pharmacokinetic parameters of amoxicillin in serum following regimen I and regimen II were not significantly different (p > 0.05). The mean Cmax values were 14.62 +/- 5.39 and 12.65 +/- 4.76 micrograms/ml, the Tmax were 2.3 +/- 1.0 and 2.0 +/- 0.9 hour and the AUC0-6 were 40.79 +/- 13.26 and 38.75 +/- 15.04 micrograms/ml.h in the group I and group II, respectively. From these results, we concluded that omeprazole has no effect on gastric mucosa level nor serum levels of amoxicillin. The therapeutic efficacy of using these two agents in the eradication regimen of H. pylori may be related to other factors rather than pharmacokinetic interaction.