Although WU polyomavirus (WUPyV) and human polyomavirus 6 (HPyV6) are widespread in adults, the long-term serological responses to these infections have not been systematically characterized. To address this gap, we assessed seroprevalence and IgG antibody stability of WUPyV and HPyV6 using data from the Finnish Family HPV (FFHPV) study, initiated in 1998. The cohort included 318 women in their third trimester of pregnancy and 133 male spouses, with follow-up samples available from 281 women and 119 men at 12, 24 and 36 months. IgG antibodies against the VP1 capsid proteins of both viruses were measured using Multiplex Serology. Persistent seropositivity was high for both WUPyV (97.5% in both sexes) and HPyV6 (66.9% in women; 72.3% in men), with antibody levels remaining stable over time. Men consistently exhibited significantly higher WUPyV and HPyV6 IgG antibody levels compared to women (p < 0.033 and 0.003, respectively). A history of miscarriage was significantly associated with reduced odds of persistent HPyV6 seropositivity (OR 0.45 (95% CI: 0.21-0.97)), while other examined co-factors showed no significant associations. Antibody levels between spouses were not correlated, and pregnancy had no effect on maternal antibody levels. These findings demonstrate that WUPyV and HPyV6 infections are common, with long-lasting IgG responses, and suggest a potential link between miscarriage and HPyV6 serology that warrants further investigation.