This study aimed to compare worries related to the Coronavirus disease 2019 (COVID-19) in families with young children in two regions in Germany differently affected by the pandemic (Regensburg in Southeast Germany, Leipzig in Eastern Germany) during the first and the second waves of the COVID-19 pandemic. 720 parents participating in the KUNO Kids health study in Regensburg (n = 507) or the LIFE Child study in Leipzig (n = 213) answered questions regarding COVID-19-related worries and trust in anti-pandemic policy measures during the first wave (spring 2020) and during the second wave (winter 2020/2021) of the pandemic. Ordinal mixed-effects models were performed to assess differences depending on region and time, adjusting for education and migration background. Participants worried most about the general economic situation and their family and least about their own health or financial situation. Worries about oneself, family, friends, hometown, and country were stronger during the second than during the first wave. In regional comparisons, worries about family, friends, and hometown increased more pronouncedly from wave 1 to wave 2 in Leipzig (OR ranging from 2.67 (95% CI 1.71-4.19) to 3.01 (95% CI 1.93-4.71), all p < 0.001) than in Regensburg (OR ranging from to 1.38 (95% CI 1.08-1.78) to 1.72 (95% CI 1.33-2.21), all p < 0.05), running parallel with the increase in SARS-CoV-2 infections. Trust in anti-pandemic policy measures, in contrast, decreased significantly between wave 1 and wave 2, with a stronger decrease in Regensburg (OR = 0.30 (95% CI 0.22-0.39), p < 0.001) than in Leipzig (OR = 0.91 (95% CI 0.59-1.41), n.s.). The degree of families' COVID-19-related worries differs by region and time, which might be related to differences in infection rates and public interest. Regional differences should be taken into account when developing communication strategies and policy measures during the COVID-19 pandemic.