Metal stress is among the important environmental stresses, which influences the growth and development of plants and crops in many areas in the biosphere. Root is an important gate for the absorption of water and mineral nutrition which in many types of lands is also accompanied by a higher concentration of metal elements, either essential (such as Fe, Mn, and Cu) or non-essential metal elements or heavy metals (such as Al, Pb, Hg, Cd, and Ag). In response to metal stress, plant roots sometimes develop a cellular structure to prevent excessive concentration of metal components to avoid toxic effects and cellular damage. Physiological and biochemical responses at the cellular level, which result in ultrastructure changes may occur due to or to avoid the negative effect of metal toxicity. In many cases it was followed by the reduction of root growth followed by discontinuing entirely plant growth. On the other hand, the structural changes are an important part of root mechanism to sustain the plant from metal toxicity. In this chapter, different changes in the cellular ultrastructure resulting from toxic damage or indicating tolerance response to metal stress will be elucidated.