A well-developed root system is a very important characteristic of rootstocks. Initial plant characterization is a potential technique to highlight cultivars with desirable root architecture for the diversification of rootstocks in the national citriculture. Thus, the aim of this study was to evaluate the initial shoot development and root architecture of citrus cultivars used as rootstocks. Seeds from five rootstocks, ‘Cleopatra’ mandarin, ‘Rangpur’ lime, ‘Rough’ lemon, ‘C13’ and ‘Troyer’ citranges, were sown in black polyethylene bags. A completely randomized block design with five replications and one plant per plot was applied. At 30 and 45 days after emergence, shoots and roots were collected for analysis. Shoot analysis measured the total number of leaves, leaf area, stem diameter, plant height, and fresh and dry matter weights. Root analysis evaluated fresh and dry matter weights and root architecture by image analysis, which recorded root traits including primary, secondary, and tertiary root numbers; length and total volume; and the percentage of secondary roots present in the upper third of the primary root. Shoot and root data of fresh and dry weights were submitted to variance analysis and compared using Tukey’s test (5%). The remaining root data were standardized for variance 1 and studied through principal component analysis. The ‘C13’ citrange showed good shoot development, with greater leaf area, plant height, stem diameter, and shoot fresh and dry matter weights during both evaluation periods, followed by the ‘Troyer’ citrange. The ‘Cleopatra’ mandarin had the smallest shoot and root development during both evaluation periods, presenting lower primary root, secondary root, and root volume than other cultivars evaluated at the same time. The ‘Troyer’ citrange had fewer roots in the upper third of the primary root and a higher root insertion angle.