A simple flatbed-scanner-based image acquisition system was developed for the measurement of `Gala'/M9 (Malus ×domestica Borkh.) apple tree root growth in rhizoboxes with a transparent acrylic sheet on one side. A tree was planted in the center of each rhizobox, and a modified flatbed scanner was periodically used to directly capture high-resolution digital images of roots growing against the transparent wall. Total root length in the images was either measured manually, or by computer mouse tracing, or automatically with a computer image analysis system. Correlations were made among the different measurements. High quality root images were obtained with the adapted scanner system. Significant linear relationships were found between manual and computer traced root length measurements (r = 0.99), traced and automatic measurements (r = 0.76) and manual and automatic measurements (r = 0.75). Apple roots appeared on the transparent wall 34 days after transplanting, and grew rapidly thereafter, reaching a maximum on the transparent wall 59 days after transplanting. Our results showed that the use of a flatbed scanner for the acquisition of root images combined with computer analysis is a promising technique to speed data acquisition in root growth investigations.