The relationship between Helicobacter pylori infection and/or gastric disorders and chronic kidney disease (CKD) has not been elucidated. We investigated the relationship between Helicobacter pylori and/or atrophic gastritis (AG) and chronic kidney disease. In total, 3560 participants (1127 men and 2433 women) were eligible for this cross-sectional study. We divided participants into four study groups: with/without Helicobacter pylori infection and with/without AG. The HP (+) AG (−) group demonstrated a significant association with CKD compared with the HP (−) AG (−) group (adjusted odds ratio, 1.443; 95% confidence interval, 1.047–1.989). In contrast, the HP (+) AG (+) group showed significantly lower adjusted odds of CKD than the HP (−) AG (−) group (adjusted odds ratio, 0.608; 95% confidence interval, 0.402–0.920). H. pylori infection without AG might be associated with CKD in these participants. Conversely, the HP (+) AG (+) group had lower odds of CKD. Uncovering an association between gastric and renal conditions could lead to development of new treatment strategies.