Methods for diagnosing chronic diarrhea and other gastrointestinal conditions. In the methods, a sample of gastrointestinal secretions is obtained from a control group； or a group who has been diagnosed with either healthy gastrointestinal tracts or with a gastrointestinal condition, like chronic diarrhea. The control group samples are analyzed in any suitable manner to determine the levels of gastrointestinal secretions, including one or more autophagy-related proteins, cytokeratins, digestive enzymes, or other proteins. The results of the sample analysis are used to create a database containing profiles of normal and abnormal gastrointestinal secretions. As the database is created and specific secretion level abnormalities are identified, patients may be diagnosed with these abnormalities and be treated by adjusting the levels of specific secretions. Gastrointestinal samples from subsequent patients may be analyzed and compared with the database to determine which of the patients' secretion levels, if any, are abnormal.
