Torque teno viruses (TTVs) are classified into the Anellovirus genus of the Circoviridae family. In addition to TTV isolates, TTV genogroup 3 also includes the 8 virus strains known as SENV-A to H. In this study, the prevalence of TTV group 3 viruses and that of SENV-D and H in particular were determined among the staff of a hospital in Budapest. Viruses were genotyped using type-specific PCR primers and by cloning and sequencing of PCR products. Frequency of infection with TTV group 3 was high among both the hospital staff and the control group. Prevalence of SENV-H was similar in the two groups, but SENV-D infection was significantly more common in the study group than in controls. Sequencing of PCR products showed that viruses closely related to isolate TUS01 are common in Hungary. Several sequences could not be genotyped and may represent a previously undescribed genotype within the genogroup. TTV group 3 sequences detected in the serum samples of a symptomless health care worker were followed-up for 15 years. Some strains persisted for up to 10 years, while others caused transient infections and could be detected in only one of the samples. Results showed that TTV infection, superinfection, and viral clearance often occur over the years without apparent symptoms.