Background Although human bocavirus type 1 (HBoV1) is a respiratory pathogen, presence of HBoV-DNA in secretions of asymptomatic children raised the question on the significance of HBoV-positive results. Methods Archived specimens from a prospective, longitudinal study were tested for HBoV. A total of 94 children (aged 6 – 36 m) were HBoV(+) during 172 upper respiratory tract infection (URI) and/ or acute otitis media (AOM) episodes. We used pyrosequencing of NP1, VP1 and VP2 genes to type HBoV and subtype HBoV1 in these specimens. Results Of the specimens tested, HBoV-DNA were successfully sequenced in 128 (74%) samples from 70 children; all were HBoV type 1. Subtypes identified (n=108) were: LWK/TW (63%), LWK/BJ (20%), Bonn/BJ (16%) and LWK/KU3 (1%). Of 46 children for whom shedding pattern could be determined, viral clearance within 30d (13-29d) occurred in 28%; another 22% of children had no recurrence after 32 to 267d. Prolonged virus presence of >30 d (34 to 181d+) occurred in 22%; intermittent detection (61+ to 170d+) in 20%. Infection with the same HBoV1 subtype after 4-5 negative samples (244 and 265d interval) occurred in 4%. Infection with 2 different HBoV1 subtypes (29 and 87d apart) occurred in only 4%. Newly acquired HBoV1-URI resulted in AOM in 53% of cases. Conclusions Children with HBoV1 infection commonly shed for a prolonged period leading to repeated viral DNA detection. Recurrence after 8-9 m suggests possible persistence and reactivation. Infections with 2 different HBoV1 subtypes within one-year period are uncommon. Newly acquired HBoV1-URI is often complicated by AOM.