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Viral infection may trigger islet autoimmunity, type 1diabetes (T1D), or both. Fluctuating population density of bank voles as a putative reservoir of Ljungan virus has been claimed to be associated with variations in T1D incidence rate (IR). We tested the hypothesis that Ljungan virus antibodies reflecting prior exposure(s) to the virus may be associated with islet autoimmunity, childhood diabetes or both. Incident, 0-18y, T1D patients (n = 63) were studied along with age and sample time matched controls (n = 126). The younger children (< 9 years) tended to have a higher incidence rate during winter (IR = 67.6, 95%CI 41.9-103.5) compared to summer (IR = 33.6, 95%CI 15.3-63.9) months. The proportion of children with high level antibodies against Ljungan virus (LVAb) were both younger compared to the rest of the children (p < 0.002) and correlated with half yearly T1D IR (r = 0.78, p = 0.005). High level LVAb fluctuating with season and correlating with T1D IR indicates that past exposure to Ljungan virus may be associated with T1D.