In allogeneic bone marrow transplanted (BMT) patients BK virus (BKV) reactivation has been associated with haemorrhagic cystitis (HC). However, it is far from obvious which patients will develop HC, since BKV, a human polyomavirus, is ubiquitious and infects children at an early age. To investigate if a primary BKV infection, as such or possibly due to transmission of BKV by the marrow graft during BMT, was correlated to the development of HC, 45 children were followed for possible BKV seroconversion and development of HC at different time points after BMT. Serum samples were collected from the 45 allogeneic BMT children and their donors before transplantation, and from the patients at 3, 6 and 12 months after BMT. These sera were analysed for the presence of specific antibodies towards BKV by hemagglutination inhibition (HAI) and by IgG- and IgM-class specific enzyme linked immunosorbent (ELISA) assays. Twelve of the 45 BMT children had a documented episode of HC or hematuria. All patients and 98% of the donors were HAI positive before BMT, while with ELISA 87% of the patients and 84% of the donors were positive. Moreover, most HC and hematuria children (11/12) were seropositive with both assays before BMT, making it impossible to investigate possible BKV transmission through the bone marrow graft during BMT by serology. Still, serological changes such as ELISA seroconversion, IgM antibodies and/or HAI titer increases were significantly (p=0.016) more common in patients with HC (58%) than without HC (24%), but these changes occured mainly after HC symptomatology had already resolved. However, there was a near significant difference (p=0.053) in BKV seroprevalence by ELISA among the donors of patients with HC or hematuria (67%) as compared to the donors (91%) of patients without HC.