Currently, there are only few data on health literacy in patients with chronic gastrointestinal diseases such as gastrointestinal cancer, inflammatory bowel disease (IBD) and, in particular, liver cirrhosis available. Moreover, head-to-head comparisons between patients with these different diseases are lacking. In this study, 379 patients were enrolled. Of these, 102 patients had gastrointestinal cancer, 86 had IBD, and 191 had cirrhosis. Health literacy was quantified using the Health Literacy Questionnaire (HLQ) developed by Osborne et al. (Swinburne University, Australia) and was compared between these three groups. Patients with cancer had the best health literacy across all nine subscales of the HLQ, while patients with cirrhosis had the poorest. In detail, patients with cirrhosis had significantly poorer health literacy than patients with cancer or IBD in subscales such as “feeling understood and supported by healthcare providers”, “having sufficient information to manage my health”, “appraisal of health information”, “ability to actively engage with healthcare providers” or “understanding health information well enough to know what to do” (p < 0.05 for cirrhosis versus IBD or cancer, respectively). In conclusion, health literacy differs remarkably between patients with chronic gastrointestinal diseases such as cirrhosis, IBD or gastrointestinal cancers.