Linum usitatissimum is a source of pharmacologically active lignans and neolignans. An effective protocol has been established for the enhanced biosynthesis of lignans and neolignans in cell cultures of Linum usitatissimum by using chitosan addition. Gene expression analysis of monolignols (PAL, CCR and CAD), lignans (DIR, PLR and UGT) and neolignans (PCBER) biosynthetic genes by RT-qPCR as well as monolignol biosynthetic PAL, CCR and CAD enzyme activities evidenced a stimulation following chitosan treatment. Validated reverse phase high-performance liquid chromatography coupled to diode array detection was used to quantify secoisolariciresinol diglucoside (SDG) and lariciresinol diglucoside (LDG), dehydrodiconiferyl alcohol glucoside (DCG) and guaiacylglycerol-beta-coniferyl alcohol ether glucoside (GGCG) showed that chitosan treated cell cultures had better accumulation of these metabolites. Maximum enhancements of 7.3-fold (28 mg/g DW) occurred for LDG, 3.5-fold (58.85 mg/g DW) in DCG and while the least enhancement of 2-fold (18.42 mg/g DW) for SDG was observed in 10 mg/l chitosan treated cell cultures than to controls. Furthermore, same concentration of chitosan also resulted in 1.3-fold increase in antioxidant activity. Compared to the lignans and neolignans accumulations observed in wild type and RNAi-PLR transgenic flaxseeds, chitosan-treated cell cultures appeared to be a very effective production system for these compounds.