Alterations in the intestinal bacterial flora are believed to be contributing factors to many chronic inflammatory and degenerative diseases, including rheumatic diseases. While microbiological fecal culture analysis is now increasingly used, little is known about the relationship of changes in intestinal flora, dietary patterns and clinical outcome in specific diseases. To clarify the role of microbiological culture analysis, researchers aimed to evaluate whether or not in patients with rheumatoid arthritis (RA) or fibromyalgia (FM) a Mediterranean diet or an 8-day fasting period are associated with changes in fecal flora and whether or not changes in fecal flora are associated with clinical outcome. During a 2-month period 51 consecutive patients from an integrative medicine hospital department with an established diagnosis of RA (n = 16) or FM (n = 35) were included in the study. According to predefined clinical criteria and the subjects’ choice the patients received a mostly vegetarian Mediterranean diet or participated in an intermittent modified 8-day fasting therapy. Quantitative aerobic and anaerobic bacterial flora, stool pH and concentrations of secretory immunoglobulin A (sIgA) were analysed from stool samples at the beginning, at the end of the 2-week hospital stay and at a 3-month follow-up. Clinical outcome was assessed with the DAS 28 for RA patients and with a disease severity rating scale in FM patients. No significant changes were found in the fecal bacterial counts following the two dietary interventions within and between groups, nor were significant differences found in the analysis of sIgA and stool pH. Clinical improvement at the end of the hospital stay tended to be greater in fasting vs. non-fasting patients with RA. Clinical outcome was not related to alterations in the intestinal flora.