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Diagnosis of bowel diseases is often difficult and time consuming since it is not always possible to obtain adequate information by the conventional diagnostic methods to set up a diagnosis and exclude nongastrointestinal causes of symptoms. The aim of this study was to investigate the structure of blood serum samples of patients with selected intestinal diseases. The blood serum samples of patients (N=35) with selected diagnoses (mesenteric thrombosis, inflammatory bowel disease, duodenal ulcers, sepsis, enterorrhagia, sigmoid colon resection, small intestine cancer) and of healthy subjects were evaluated by synchronous fluorescence fingerprint and atomic force microscopy. Autofluorescence of blood serum studied at λex = 280 nm showed significant decrease of fluorescence intensity in patients with all types of diseases affecting bowels in comparison with the healthy control patients. The blood serum surface of ill patients showed significant differences in comparison with control group samples after atomic force microscopy evaluation as well. Irregularly placed small globular units of irregular shape in small amounts are possible to observe in patients with intestine ischemia. Fluorescence analysis and atomic force microscopy showed the ability to rapidly reflect qualitative and quantitative changes of proteins in blood serum samples of patients. These sensitive methods could be beneficial for monitoring the progression of both acute or chronic bowel diseases.