Background: Diarrhea is a frequent problem among persons with advanced HIV disease. In the absence of treatable pathogens, symptomatic relief is all that is available for current therapy. As a result, many patients with HIV and chronic diarrhea have turned to herbal formulas for treatment. We assessed the effectiveness and safety of a Chinese herbal formulation (Source Qi) in reducing the number of stools per day related to HIV-associated, pathogen-negative diarrhea. Methods: Sixteen male patients received treatment with Source Qi in an 8-week, open-label study. Patients tested negative for cryptosporidium and other gastrointestinal pathogens, and had chronic diarrhea, defined as having three or more loose stools/day for >/=14 days (and no other treatable causes for diarrhea). Measurements of diarrhea included numbers of bowel movements/day, abnormal bowel movements/day, and liquid bowel movements/day. Subjects completed daily stool diaries an average of 2 weeks before and up to 8 weeks after starting Source Qi. Paired Wilcoxon tests compared the last week before treatment with each week of treatment. Results: There was a reduction in average number of stools/day in each week of treatment (-0.2 to -0.8), except week 1 (+0.1), with improvements in weeks 2-6 approaching or reaching statistical significance. Conclusions: A modest but sustained decrease in average number of stools/day was observed in patients with HIV-associated, pathogen-negative diarrhea. The entry criteria, 2-week run-in period, lack of benefit in week 1, and sustained benefit thereafter all suggest that the improvement was not due to bias.