The aim of the present study was to investigate hair essential trace elements and mineral levels in 105 pregnant normal-weight (control) and 55 overweight and obese women in the third trimester of pregnancy, as well as in their children at the age of 9 months. The hair essential trace elements and mineral levels were assessed using inductively coupled plasma mass-spectrometry. Overweight pregnant women had significantly reduced Cr (− 24%; p = 0.047) and Zn (− 13%; p = 0.008) content, as well as elevated hair Na and K levels as compared to the controls. Children from overweight and obese mothers had lower hair Mo (− 18%; p = 0.017), Se (− 8%; p = 0.043), and V (− 24%; p = 0.028) levels, as well as elevated Sr content (19%; p = 0.025). Correlation analysis revealed a significant relationship between maternal and child hair levels of Co (r = 0.170; p = 0.038), Cu (r = 0.513; p < 0.001), Mn (r = 0.240; p = 0.003), and Na (r = 0.181; p = 0.027) in the whole sample. Pre-pregnancy maternal body mass index (BMI) positively correlated with maternal hair K (r = 0.336; p < 0.001) and Na (r = 0.212; p = 0.008) and negatively correlated with V (r = − 0.204; p = 0.011) and Zn (r = − 0.162; p = 0.045) levels. The results indicate that impaired trace element and mineral metabolism may play a role in the link between maternal obesity, complications of pregnancy and child’s postnatal development. Hypothetically, dietary improvement may be used as a tool to reduce these risks. However, further experimental and clinical studies are required to investigate the relationship between obesity and trace element metabolism in pregnancy. © 2019, Springer Science+Business Media, LLC, part of Springer Nature.