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There are differences between HelpDesk for JIRA and JIRA ServiceDesk:

	JIRA Service Desk	HelpDesk for JIRA
Free users for Customers			Both plugins provide free customer accounts. Customers (Reporters) can login to Personal Customer Area, but they can not login to JIRA interface.
Personal Customer Area			Customers have private area for creating and searching own issues. At HelpDesk customers may see not only they own issues, but other issues, which they have permission to see.
Free Agents			You must buy license for your all users who wants to assign, comment and move issues through process when you use JIRA Service Desk. So, it is very expensive solution if you have more than 5 people in first and second line of your support team. HelpDesk for JIRA doesn't have Agents. So, all of your JIRA users can process issues for free without any limitations.
Knowledge base integration			JIRA Service Desk provides simple integration with just one knowledge base - Confluence. How does it work? When reporter create new issue, JIRA Service Desk show him some Confluence paged fitted for entered issue summary. HelpDesk doesn't provide any integrations, but we have a lot of plans here. Stay connected.
Preventing Duplicates Issues			HelpDesk shows issue's duplicates while user is creating a new issue. Service Desk doesn't have this feature.
SLA Management			Both plugins provide SLA mechanism. It can help you control resolution time for specific conditions.
SLA Reports			JIRA Service Desk provides simple reports mechanism. But it has is poor and limited metrics for reports. Just like: Average Time and Breached Time. There is no way to extend these reports. HelpDesk doesn't provide any reports at this moment, but we have a lot of plans here. Stay connected.
CRM for JIRA integration			With Helpdesk&CRM it's very easy to arrange Customer Support based not on single users but on Companies. At Helpdesk portal, you may set a separate tab for user's company issues. At JIRA you may create different reports that will show Companies Support statistics.
Change notification scheme			At Helpdesk it's possible to set Customer notification rules flexible. ServiceDesk has in-build notification schema for notifications, that can not be changed.
Direct private links in emails			You can enable private links to Jira issues in emails. It helps users go to issues through email without login. Very quick, very simple and safe.