We examined patterns of seedling root architecture, morphology and anatomy in Australian perennial plants chosen as phylogenetically independent contrasts (PICs) for rainfall in the areas they inhabit. Our objective was to assess whether there are consistent evolutionary patterns in structure of seedling root systems in species from different rainfall environments when examined across multiple evolutionary lineages. Seedlings were grown to a standardised developmental stage under controlled conditions. We found that seedling root systems of species restricted to low rainfall environments are characterised by greater proportional allocation to main root axis and have proportionally smaller main root axis diameter and areas of stele and xylem. Species of low rainfall environments also had higher specific root length (SRL) of the main axis, but lower SRL when the entire root system was considered. Seedling root system elongation rates were higher in species of high rainfall relative to those of low rainfall environments, paralleling expected differences in relative growth rate. The higher root system elongation rates in species of high rainfall environments were associated with greater numbers of growing tips in the root system, but not with differences in elongation rates of individual tips, relative to species of low rainfall environments.