The development of biomaterials has increased rapidly in order to alter the fate of stem cells and use them in therapeutic applications. Currently, many biomaterials are used in the biomedical industry. Biomaterials act as a “nitch” which is an environment regulating the development and self-renewal behaviour of stem cells. The stem cells receive signals from the “nitch” and proceeds accordingly. In order to control the behaviour of stem cells, the chemical and physical properties of the biomaterial should be taken into consideration. This review paper focuses on the different type of metals used in biomaterials, identifying their current issues and challenges including fatigue, corrosion resistance, and the toxicity caused by metal ions released in the body. It also provides detailed explanations about the impact of various metal implants such as stainless steel, cobalt-chromium, and titanium on stem cells and the toxicity caused by the interaction of biomaterials and various trace elements with the hostile body environment.