Infection with human polyomaviruses BKV and JCV is asymptomatic, and lifelong and widespread, among the general population. However, in the setting of immunosuppression, secondary to medications or viral infection, for example, with HIV, reactivation can occur and result in severe disease. In this study, stool specimens from 31 patients with hematological disorders (25 transplanted and 6 non-transplanted) were examined prospectively to determine whether the novel polyomaviruses KIV and WUV reactivated and were excreted in the gastrointestinal tract. Reactivation was correlated with the appearance of gastrointestinal and respiratory symptoms. Of the 31 patients examined, KIV and WUV were detected in 13 transplanted patients as single infection or in combination with BKV, cytomegalovirus (CMV), and adenovirus (Adv). Because of frequent co-infections, a clear correlation between novel polyomaviruses and clinical symptoms could not be established. There was no correlation between demographic variables and detection of KIV and WUV. Phylogenetic analysis of the small t-antigen gene of KIV and WUV isolates showed that the novel polyomaviruses identified in feces clustered with those identified in the respiratory tract suggesting an oral-fecal transmission of these viruses. The novel polyomaviruses KI and WU may have a pathogenic role in immunocompromised patients.