Objective To describe the use of Lactobacillus by hospitalized patients and to examine its relationship with various Clostridium difficile infection (CDI) related outcomes. Methods The characteristics of Lactobacillus users and non-users and the initiation of Lactobacillus with respect to initiation of antibiotic therapy and CDI treatment were described using national hospital discharge database. The relationships between Lactobacillus use and post-CDI length of stay, mortality, switch of CDI therapy, and readmission were analyzed. Results Lactobacillus users and non-users were different in most characteristics. Metronidazole and fluoroquinolones were the most frequently used antibiotics by Lactobacillus users. They were mainly CDI cases, used multiple antibiotics, extremely ill, and started Lactobacillus five or more days after initiation of antibiotics or CDI treatment. Lactobacillus use was associated with increased length of stay and switching of CDI therapy. Conclusions The true association between Lactobacillus use and CDI remains unclear. This study provides foundation for future research.