Drought during the vegetative development is usually one of the limiting factors to sugarcane yield. Information on responses of above- and below-ground parts of sugarcane plant would be useful in explaining the drought-resistant mechanism and improving genotypes for high productivity under drought conditions. Therefore, the objective of this study was to investigate the response of rooting and physiological traits to water stress at early growth stage conditions of three sugarcane cultivars. The experiment was conducted under pot conditions using a 2 x 3 factorial in randomized complete block design with four replications. Two water regimes were assigned as factor A, i.e., well-watering control and water stress at early growth stage, and three commercial sugarcane cultivars, reported to be drought resistant, were assigned as factor B shoot dry weight, cane height, stalk diameter, rooting traits such as root volume, root length, root surface area and root/shoot ratio and physiological traits, namely stomatal conductance, SPAD chlorophyll and chlorophyll fluorescence, were measured during drought and re-watering periods. Different responses to natural water deficit during the formative growth phase conditions occurred in the three sugarcane cultivars. Roots and physiological responses such as root length, chlorophyll fluorescence and stomatal conductance at stressed period were important factors contributing to sugarcane biomass yields. In addition, the partitioning of assimilate, i.e., root/shoot ratio during drought and recovery period, was a key trait for maintenance of cane biomass. The contribution of more proportion of assimilates to shoot at re-watering period is a preferred character. This information will be useful in explaining appropriate mechanisms and recommendation of the surrogate traits for improving sugarcane genotypes in breeding program for drought at early growth stage resistance.