Screening genotypes at early growing stage is considered important to breeders and researches in crop improvement. A set of 101 wheat genotypes were grown in optimum environment at the onset of two-leaf stage, 10 days after germination, in a hydroponic phenotyping system. This study aimed to characterize phenotypic variability in wheat root and shoot morphological traits at early vegetative stage and to determine the relationship among shoot and root traits. Considerable phenotypic variation existed for seminal roots length, root angle (measured between the first pair of seminal roots) and branching depth of primary root. Strong positive correlations were identified for some key root traits (i.e., root length, root dry mass, and root specific weight) and shoot traits (i.e., shoot dry mass and shoot specific weight). The cluster analysis, based on observed traits, showed the homogeneity of genotypes originating from the region of the South-East Europe. A subset of 18 genotypes with different/exceptional root and shoot characteristic have been chosen as parents for 16 targeted crosses to produce novel germplasm in wheat for improving early vigour and tolerance to drought. The average hybrid vigour across all combinations and traits under osmotic stress was -2.3% and 8.5% in non-stress and osmotic stress conditions, respectively. No one crossing combination showed positive hybrid vigour for all traits.