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Background: Helicobacter pylori (H. pylori) is the most common chronic bacterial infection in the world, affecting over 50% of the world’s population. H. pylori is a grade I carcinogen, responsible for the development of 89% of noncardia gastric cancers. In the present study, we analyzed the data for H. pylori eradication treatments in Slovenia after the 3rd national recommendations were implemented. Patients and Methods: Slovenia is part of the European Registry on H. pylori Management since the Registry was launched in 2013. Data were collected at Asociación Española de Gastroenterología-Research Electronic Data Capture electronic case report form from September 2017 to December 2019. H. pylori eradication treatment was assessed by modified intention-to-treat (mITT) and per-protocol analyses. Results: Overall, 853 patients from 3 medical institutions were included. Effectiveness with first-line 14-day triple therapy with a proton-pomp-inhibitor (PPI), clarithromycin 500 mg, amoxicillin 1,000 mg, all BID, was 93% by mITT (714 patients). In patients allergic to penicillin, first-line 14-day triple therapy with PPI-clarithromycin-metronidazole achieved 83% effectiveness by mITT (35 patients). Second-line 14-day triple therapy with a PPI-amoxicillin-levofloxacin achieved 89% mITT eradication rate (51 patients). Second-line therapy with the 10-day three-in-one single capsule containing bismuth-tetracycline-metronidazole achieved optimal effectiveness (100% mITT) in 10 patients (p = 0.02). Conclusions: Slovenia is a country with <15% H. pylori resistance to clarithromycin. Triple therapy with a PPI plus 2 antibiotics during 14 days reported optimal effectiveness (over 90%). Ten-day quadruple-bismuth second-line therapy had better results than 14-day triple therapy with levofloxacin.