Rooting media used in current root phenotyping studies can have substantial effect. In this study, the effects of three different nutrient conducting papers (Black construction paper, Anchor blue germination paper and Kimpak paper) and soil-filled boxes on root growth and root system architecture (RSA) of Brassica rapa (cultivars ‘R500’ and ‘IMB211’) were investigated. Seedlings of the two B. rapa genotypes were supplied with nutrients on the nutrient conducting papers and in the soil-filled boxes. The papers and soil-filled boxes were fixed to flatbed scanners and two-dimensional images of roots were periodically taken and analysed. Root media effects on shoot and root biomass and on topological indices (TI) were observed. For example, root branching was more pronounced on the construction paper. Mean TI of 0.82 and 0.93, recorded for R500 and IMB211, respectively, on the construction paper indicated that substrates affect the herringbone pattern of brassica roots. Whilst it was indicated that different results could be obtained for the same RSA when different germination papers are used, the results showed that Anchor blue germination paper is an ideal proxy for soil in phenotyping seedlings for RSA traits and root growth.