Helicobacter pylori infection is clinically associated with dyspepsia, gastric and duodenal ulcers, and gastric cancer. Increasing antimicrobial resistance in H. pylori is a worldwide problem and failure of eradication with standard triple therapy (high-dose proton pump inhibition, amoxicillin and clarithromycin) is directly related to the presence of a resistant strain. Other treatment combinations have been investigated, but with inconsistent results. Based on a review of the recent literature in conjunction with an analysis of the regional resistance data, we address the increasing complexity of H. pylori eradication therapy. Culture and susceptibility results of all first H. pylori isolates of adults (> 18 years) seen in the Leiden University Medical Center, from January 2006 to December 2015, were analysed (n = 707). An increase in clarithromycin resistance was observed from 9.8% to 18.1% (p = 0.002) in the periods from 2006-2010 and 2011-2015, respectively. For ampicillin the resistance increased from 6.3% to 10.0% (p = 0.37), and for metronidazole from 20.7% to 23.2% (p = 0.42). The tetracycline resistance remained low at 3.2% and 2.3%, respectively. The treatment paradigm is shifting towards individualised treatment rather than a one-strategy-fits-all approach. In case of treatment failure it should be strongly considered to refer a patient for endoscopy, biopsy and culture. Thereafter, targeted antimicrobial treatment based on susceptibility results can be initiated. Furthermore, accumulating data indicate that prolongation of treatment to 14 days, as opposed to the current standard 7 day course, contributes to a higher H. pylori eradication rate.