Improving the waterlogging tolerance of wheat varieties could alleviate yield constraints caused by excessive rain and poor soil drainage. In this study, we investigated root and shoot growth as well as anatomical traits of six spring wheat genotypes with contrasting waterlogging tolerance properties. Our aim was to identify root traits that differentiate tolerant from sensitive genotypes. Two experiments were conducted using rhizoboxes and photography for data acquisition. In experiment one, root growth of the genotypes was studied during seedling establishment and a subsequent waterlogging treatment, starting at the 3-leaf stage and maintained for seven days. In the second experiment, root and shoot growth of previously waterlogged plants was compared between the genotypes during seven days of recovery. At harvest of experiment two, root segments were sampled to investigate genotype differences of root cross sectional area, root cortex area, stele area and percentage of aerenchyma. The results show that tolerant, in contrast to sensitive genotypes, developed seminal roots faster in the seedling establishment phase and more nodal roots during the waterlogging treatment. NK93602 and Bjarne were the best performing genotypes. Bjarne in particular had a narrower relative stele size of nodal (13.4%) and seminal roots (11.7%) compared to other genotypes (e.g. 16.3% in nodal roots and 13.9% in seminal roots of sensitive Quarna). The results from this study suggests that early vigor is an important trait for waterlogging tolerance in the field. Anatomical root traits, such as a narrow stele and aerenchyma may contribute to improving waterlogging tolerance furthermore.