Background: Gastrointestinal illness is a common risk for wilderness travelers, even among those who consistently disinfect their water, yet the importance of hygiene has not been characterized. Methods: In a prospective surveillance study, 334 Appalachian Trail backpackers who hiked for at least 7 days in 1997 were interviewed. Upon completion of their hike, a written questionnaire was sent, addressing illnesses, water disinfection methods, and hygiene. Hygiene inquiries focused on the frequency of behaviors concerning handwashing and cleaning cookware. Results: Two hundred and eighty backpackers compiled 38,940 wilderness exposure days, with 56% (n = 156) experiencing diarrhea. Diarrhea correlated with the frequency of drinking untreated surface water (relative risk (RR) 2.4, 95% confidence interval (CI) 1.0-4.7%, p =.03). Of those who consistently treated water, 45% suffered from diarrhea, whereas 69% of those who inconsistently treated water experienced diarrhea (RR 0.65, 95% CI 0.53-0-81%, p = .001). Hikers practicing "good hygiene", defined as handwashing postdefecation and cleaning cookware routinely, were less likely to ever experience diarrhea (RR 0.47, 95% CI 0.22-0.99, p =.04). Routine handwashing with soap and water after both urination and defecation reduced the risk of diarrhea (RR 0.11, 95% CI 0.04-0.31%, p <.001). In a case-control analysis of those experiencing diarrhea, decreased diarrhea was associated with routine consumption of multivitamins (RR 0.50, 95% CI 0.37-0.66%, p <.001), routine cleaning of utensils with warm, soapy water (RR 0.38, 95% CI 0.20-0.74%, p <.01), and postdefecation handwashing with soap and water (RR 0.61, 95% CI 0.39-0.93%, p =.006). Conclusions: Lack of hygiene, specifically handwashing and cleaning of cookware, should be recognized as a significant contributor to wilderness gastrointestinal illness. Hikers should routinely disinfect water and avoid untreated surface water.