Helicobacter pylori (H. pylori) infection (HPI) is one of the most widespread diseases. More than half of world population is affected by HPI, especially children in developing countries. The associations between many gastrointestinal diseases and HPI have been found in clinical. Also, there are some diseases whose HPI associations are controversial and unclear. Due to its unclear disease association, H. pylori test is not included in the clinical screening. However, some pre-clinical studies showed possible associations between HPI and these diseases, involving pathological changes of different functional systems of the human body (e.g., Immune system, cerebrovascular system). Therefore, for HPI patients, more attention should be paid to the possible risks of these diseases. In this study, a systematic literature review was conducted to identify and classify H. pylori related diseases. This review identified 175 HPI related diseases belonging to 9 categories, and summarized the corresponding supporting literature reports. In addition, the functional mechanisms underlying the linkages between HPI and 28 well studied diseases were discussed, revealing possible pathogenesis for these diseases. We conclude that HPI is related to many serious diseases affecting multiple important human systems, and clinical HPI treatment and HPI test might help the detection and treatment of these diseases. Our results guarantee further study using more data to testify the possible relations between HPI and these diseases.