This chapter reviews the literature on somaclonal variation affecting the micropropagation through somatic embryogenesis. The first part covers the following aspects i) principle, protocols and applications of somatic embryogenesis and ii) epigenetic reprogramming and changes in cell fate that underlie somatic embryogenesis. The second part addresses the problem of somaclonal variation in somatic embryogenesis by first i) assessing their impact on somatic embryo-derived plant production and ii) describing the multiple origins of somaclonal variation (chromosomal aberrations, genetic alterations, epigenetic regulations, transposable elements). The last part focuses on how managing somaclonal variation in commercial productions of SE-derived plants by covering different aspects, i) detection of undesirable phenotypes: screening out the variants, ii) strategies of avoidance and incidence limitation, iii) generation and exploitation of desirable phenotypes in plant breeding, iv) beyond the induction of stress-tolerant somaclonal variants: a plant breeder's perspective.