In woody plants, the juvenile-to-adult transition occurs when the apical and lateral branches reach a sufficient distance from the roots. In olive trees, there is a minimum distance required between the root and the meristem for flowering to occur. However, the way in which the roots may influence the apical meristem to develop juvenile or adult branches is still unknown; despite that, it is of great relevance for breeders. In addition, as in most fruit trees, olive cultivars are propagated by cuttings, while genetic breeding is performed by seedlings. The roots of both types of plants, cuttings, and seedlings, originate from different tissues, giving rise to differences between the two types of roots. For these reasons, we have studied the gene expression differences between the two types of roots in olive plants by microarray hybridization and found 253 genes differentially expressed, 126 over-expressed in roots of adult cuttings, and 127 in roots of juvenile seedlings. The genes over-expressed in cutting roots showed a similar distribution of genes in metabolic and biosynthetic processes, but juvenile seedling roots showed 20 % of over-expressed genes associated with lipid biosynthesis and metabolism processes, while these processes were absent in the over-expressed genes of adult cutting roots and in general, seedling over-expressed root genes are more diverse and evenly distributed than in cutting roots. In addition, eight root-specific genes have been identified.