Methods for diagnosing chronic diarrhea and other gastrointestinal conditions are disclosed. In the methods, a sample of gastrointestinal secretions may be obtained from a control group; or a group of people who have been diagnosed with either healthy gastrointestinal tracts or a gastrointestinal condition, like chronic diarrhea. The samples from the control group may be analyzed in any manner to determine the levels of secretions, like antimicrobial proteins, mitochondria, and digestive enzymes, in gastrointestinal secretions. The results of the sample analysis may be 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. Furthermore, gastrointestinal samples from subsequent patients may be analyzed and compared with the database in order to determine which secretion levels, if any, are abnormal.
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