Callus-derived cells sometimes fail to generate secondary metabolites and even when they do so in many cases the initial spurt in secondary metabolite production slowly declines and comes to a halt. However, on organogenesis, they continue to accumulate secondary metabolites. Since in whole plants production and storage of secondary metabolites is regulated by and associated with different developmental stages, organ culture appears to be a more feasible alternative to continuous large-scale production of plant secondary metabolites.

It is to be observed that many valuable and much needed phytopharmaceuticals are predominantly accumulated in bark and root tissue. Roots are an important storage organ for a variety of edible and nonedible phytochemicals. This observation led to attempts to maintain continuously growing root cultures.

It was found that many dicotyledonous plants, when infected with the soil bacteria Agrobacterium rhizogenes, are genetically transformed due to the integration of a root inducing plasmid of the bacteria into the plants’ genome. Due to this, there is proliferative formation of roots at the site of infection. Similarly, in vitro transformation of cultured cells from plants that accumulate secondary metabolites in roots initiated proliferation of fine fibrous roots in culture. These were formed not only in the absence of a growth regulator; they also showed a very high growth rate and did not show geotropism. They showed a high degree of lateral branching and the profuse growth is accompanied by an accumulation of secondary metabolites. For example, hairy root cultures of Hyoscyamus muticus when grown in batch root cultures showed a 2500–5000 fold increase in bio mass within 3 weeks and generated tropane alkaloids in yields comparable to normal plants.

Similarly, “hairy root” culture of Valeriana officinalis var sambucifolia made valepotriates four times in yield compared to normal roots. Secondary metabolite yield in hairy roots of Lupinus species (Isoflavonoids), Peganum species (serotonin), Datura stramonium, and Duboisia myoporoides was much more than that made in suspension cultures. Production of artemisinin from transformed root cultures of Artemisia annua has been extensively studied. Co-culture of hairy roots and microbes are reported to produce unique secondary metabolites. For example, Hordeum vulgare hairy root culture infected with Vesicular Arbuscular Mycrorrhizal (VAM) fungi Glomus intra radices produced a new terpenoid glycoside. Many industrial scale reactors able to house and culture such hairy root cultures are being experimented with, to upscale the success seen in laboratory level trials.