Molecular microbiology has revolutionized the landscape of microbiology and will continue to do so by providing new solutions for microbe identification and characterization. This applies also to the study of Helicobacter pylori where current genotypic (molecular) methods are important complements or alternatives to phenotypic methods. Besides providing sensitivity and specificity and an enhancement of the detection process, they also reduce much of the subjectivity inherent in the interpretation of morphological and biological data. Another key advantage of molecular methods is that they allow the identification of novel virulence factors of pathogenic bacteria. For example, such gene products enable H. pylori to establish itself within the gastric environment and enhance its potential to cause disease. Next-generation sequencing will open up new areas of research for those involved in the field of Helicobacter research and will also provide information that will help to develop novel treatment strategies and increase our understanding of the mechanisms behind chronic inflammations in the gut. The analysis of data resulting from a large-scale sequencing project requires the use of bioinformatics, including standard BLAST analysis, annotation or clustering, and assembly competence. However, the amount of data produced by the next-generation sequencing platforms will require a bioinformatics capacity at the industrial scale, which may limit the availability of such technologies. Consequently, building effective new approaches to data analysis must be given high priority.