Background: Children are affected rather mildly by the acute phase of COVID-19, but predominantly in children and youths, the potentially severe and life threatening pediatric multiorgan immune syndrome (PMIS) occurs later on. To identify children at risk early on, we searched for antibodies against SARS-CoV-2 and searched for early and mild symptoms of PMIS in those with high levels of antibodies. Methods: In a cross-sectional design, children aged 1-17 were recruited through primary care pediatricians for the study (a), if they had an appointment for a regular health check-up or (b), or if parents and children volunteered to participate in the study. Two antibody tests were performed in parallel and children with antibody levels >97th percentile (in the commercially available test) were screened for signs and symptoms of PMIS and SARS-CoV-2 neutralization tests were performed. Results: We identified antibodies against SARS-CoV-2 in 162 of 2832 eligible children (5.7%) between June and July 2020 in three, in part strongly affected regions of Bavaria. Approximately 60% of antibody positive children showed high levels of antibodies. In those who participated in the follow up screening, 30% showed some mild and minor symptoms similar to Kawasaki disease and in three children, cardiac and neuropsychological symptoms were identified. Symptoms correlated with high levels of non-neutralizing and concomitantly low levels of neutralizing antibodies and lower neutralizing capacity. Conclusions: Children exposed to SARS-CoV-2 should be screened for antibodies and those children with positive antibody responses should undergo a stepwise assessment for late COVID-19 effects.