The objective of the study was to estimate the possible association of maternal diseases with the risk of isolated ear congenital abnormalities (IECA) including mainly microtia and anotia in their children. Incidence of acute and prevalence of chronic maternal diseases in the mothers with IECA and in the mothers of their matched controls and all controls without any defects, in addition in the mothers of malformed controls with other isolated defects was compared in the population-based large dataset of the Hungarian Case-Control Surveillance of Congenital Abnormalities. Of 354 cases with IECA, 32 had mothers with high fever related influenza-common cold during the critical period of IECA and it resulted in a higher risk of IECA in their live-born infants (adjusted OR with 95% CI: 4.3, 1.9-7.4) compared with their matched controls. However, the early and effective antifever treatment in these pregnant women prevented them from the IECA. In addition there was an association of maternal otitis media with higher risk of complex defects of middle and external ears (OR with 95% CI: 5.2, 1.6-28.3), however, this association was based on 4 cases only. In conclusion high fever related influenza-common cold with secondary complications may play a role in the origin of IECA, but is preventable with the early and effective antifever treatment of these pregnant women.