Windows Defender detects and removes known spyware only. Windows Defender is not designed to protect against full breadth of malicious software. Although Microsoft Security Essentials is not designed to replace Windows Defender, but you do not need to run Windows Defender if you are running Microsoft Security Essentials because Microsoft Security Essentials is designed to disable Windows Defender in order to manage PC’s real-time protection including anti-virus, rootkits, Trojans and spyware.
Microsoft Security Essentials should disable Windows Defender on Vista and Windows 7 and uninstall it from XP. In some cases, this does not happen automatically. You should disable Windows Defender to prevent conflicts if Microsoft Security Essentials did not automatically disable Windows Defender on Vista or Windows 7. Windows Defender cannot be uninstalled from Vista or Windows 7. If Microsoft Security Essentials did not automatically uninstall Windows Defender on XP, you should manually uninstall Windows Defender via Control Panel/Add or Remove Programs.
If Microsoft Security Essentials and Windows Defender are both running, your system may experience performance degradation and other problems caused by the conflict of two services providing real time protection simultaneously.
via Microsoft Answer