Background. In May–July 2011, Germany experienced a large food-borne outbreak of Shiga toxin 2—producing Escherichia coli (STEC O104:H4) with 3842 cases, including 855 cases with hemolytic uremic syndrome (HUS) and 53 deaths. Methods. A multicenter study was initiated in 5 university hospitals to determine pathogen shedding duration. Diagnostics comprised culture on selective media, toxin enzyme-linked immunosorbent assay, and polymerase chain reaction. Results were correlated with clinical and epidemiologic findings. Testing for pathogen excretion was continued after discharge of the patient. Results. A total of 321 patients (104 male, 217 female) were included (median age, 40 years range, 1–89 days). Median delay from onset of symptoms to hospitalization was 4 days (range, 0–17 days). Two hundred nine patients presented with HUS. The estimate for the median duration of shedding was 17–18 days. Some patients remained STEC O104:H4 positive until the end of the observation time (maximum observed shedding duration: 157 days). There was no significant influence of sex on shedding duration. Patients presenting with HUS had a significantly shortened shedding duration (median, 13–14 days) compared to non-HUS patients (median, 33–34 days). Antimicrobial treatment was also significantly associated with reduced shedding duration. Children (age ≤15 years) had longer shedding durations than adults (median, 35–41 vs 14–15 days). Conclusions. STEC O104:H4 is usually eliminated from the human gut after 1 month, but may sometimes be excreted for several months. Proper follow-up of infected patients is important to avoid further pathogen spread.