Pathogens, insects and weeds have significantly reduced agricultural productivity. Thus, to increase the productivity, synthetic agricultural chemicals have been overused. However, these synthetic compounds that are different from natural products cannot be broken down easily in natural systems, causing the destruction of soil quality and agricultural environments and the gradually difficulty in continuous agriculture. Now agriculture is faced with the various problems of minimizing the damage in agricultural environments, securing the safety of human health, while simultaneously increasing agricultural productivity. Meanwhile, plants produce secondary metabolites to protect themselves from external invaders and to secure their region for survival. Plants infected with pathogens produce antibiotics phytoalexin; monocotyledonous plants produce flavonoids and diterpenoids phytoalexins, and dicotylodoneous plant, despite of infected pathogens, produce family-specific phytoalexin such as flavonoids in Leguminosae, indole derivatives in Cruciferae, sesquitepenoids in Solanaceae, coumarins in Umbelliferae, making the plant resistant to specific pathogen. Growth inhibitor or antifeedant substances to insects are terpenoids pyrethrin, azadirachtin, limonin, cedrelanoid, toosendanin and fraxinellone/dictamnine, and terpenoid-alkaloid mixed compounds sesquiterpene pyridine and norditerpenoids, and azepine-, amide-, loline-, stemofoline-, pyrrolizidine-alkaloids and so on. Also plants produces the substances to inhibit other plant growths to secure the regions for plant itself, which is including terpenoids essential oil and sesquiterpene lactone, and additionally, benzoxazinoids, glucosinolate, quassinoid, cyanogenic glycoside, saponin, sorgolennone, juglone and lots of other different of secondary metabolites. Hence, phytoalexin, an antibiotic compound produced by plants infected with pathogens, can be employed for pathogen control. Terpenoids and alkaloids inhibiting insect growth can be utilized for insect control. Allelochemicals, a compound released from a certain plant to hinder the growth of other plants for their survival, can be also used directly as a herbicides for weed control as well. Therefore, the use of the natural secondary metabolites for pest control might be one of the alternatives for environmentally friendly agriculture. However, the natural substances are destroyed easily causing low the pest-control efficacy, and also there is the limitation to producing the substances using plant cell. In the future, effects should be made to try to find the secondary metabolites with good pest-control effect and no harmful to human health. Also the biosynthetic pathways of secondary metabolites have to be elucidated continuously, and the metabolic engineering should be applied to improve transgenics having the resistance to specific pest.