The interest in the association between feelings of guilt and shame and psychological health is growing. However, less attention so far has been paid to the associations with chronic disease. Therefore, the aim of this study was to explore whether feelings of guilt and shame are related to physical health in chronic disease and in selected ones. A nationally representative sample of Czech adults (n = 1000, age = 46.0 +/- 17.3 years, 48.6% men) participated in the survey. Feelings of guilt and shame (items from The Positive and Negative Affect Schedule) and health problems in selected chronic diseases were measured. Respondents with higher feelings of guilt - but not of shame - were more likely to suffer from a chronic disease; we found this in arthritis, back pain, cardiovascular disease, asthma, cancer and depression or anxiety. The association was strongest in the case of cancer with odds ratios (OR) 5.83 (95% confidence interval (CI) 2.27-16.69). There were no significant associations in case of diabetes and stroke. Feelings of shame were not related to chronic diseases. Our findings suggest that feelings of guilt are associated with worse physical health. Further research is needed in this area.