The structure and ultrastructure of cell aggregates and derived root primordia were analysed in established suspension cultures of Solanum lycopersicoides Dun. A total of four modified Murashige and Skoog (1962) (MS) media were used, two containing alpha-naphthaleneacetic acid (NAA) and two containing 2,4-dichlorophenoxyacetic acid (2,4-D). Considerable differences were observed in the size and structure of the aggregates regardless of the medium. The largest aggregates had a four-zone structure (cover, starch, dividing and differentiation zones) with distinct ultrastructural organization. The degree of histological and ultrastructural differentiation in the aggregates indicated rhizogenesis initiation. It begins with the protrusion of mounds of root primordia, which are the result of radial growth of cells in defined zones of the aggregate. Further growth from the primordium forms a root meristem with three tiers initial centre and wholly distinguished histogens (dermatogen, periblem, plerome). Rhizogenesis was more regular on media with NAA than on media with 2,4-D. Primordia and fully organized roots were liberated due to fragmentation of the aggregate and underwent changes in the permanently active developmental cycle of the culture which gave rise to successive generations of aggregates. Growth regulators had different influences on the organellar composition and phenolic compounds presence in the different zones of aggregates.