There are multiple test methodologies to determine the antibiogram of an organism. Standardized susceptibility test methods are based upon rapidly growing, aerobic microorganisms in which overnight incubation results in definitive endpoints. In vitro susceptibility testing for fastidious organisms that require complex media for growth, require incubation in atmospheres other than ambient air, or are slow-growing (anaerobes, mycobacteria, filamentous fungi) are problematic and in general are not standardized. H. pylori falls into this category of troublesome organisms. For the microaerobic organism H. pylori, testing is challenging because the organism grows slowly even under optimal culture conditions. Recently the National Committee for Clinical Laboratory Standards (NCCLS) approved the agar dilution method as the test of choice for testing H. pylori. While not entirely reliable in predicting the outcome of treatment for metronidazole resistant organisms, the resistance determined for clarithromycin by this method generally predicts treatment failure. Quality control breakpoints for H. pylori ATCC 43504 were established and breakpoints for clarithromycin were approved by the NCCLS in 1999. Breakpoints are minimum inhibitory concentrations (MIC) of a drug at which an organism is deemed either susceptible or resistant to the antibiotic using standard dosing regimens containing that drug. Significant progress has been made with respect to development of tests to detect antimicrobial resistance, but there still remains no consensus as to the breakpoints for agents used in the treatment of H. pylori infection other than clarithromycin. This article will address the controversies associated with the reporting of antibiotic resistance data and the interpretation of these data.