Exhibit 10.1
    

    
      The athenahealth Executive Incentive
      Plan
    

    
    	
           
        	
          
            I.
          

        	
          
            Purpose – The purpose of the Executive Incentive
            Plan (the “Plan”) of athenahealth, Inc. (the “Company”) is to:
          

        
	

        	

        	
          
            a.
          

        	
          
            attract, retain, and motivate the highest quality executives;
          

        
	

        	

        	
          
            b.
          

        	
          
            provide participants with significant incentive through focus of
            our resources on our business strategy by maximizing revenue,
            managing expenses, and enabling the Company to produce long-term
            growth, thereby increasing the Company’s value to the Company’s
            shareholders; and
          

        
	

        	

        	
          
            c.
          

        	
          
            foster a cooperative teaching and learning environment that
            focuses on delivering shareholder value, providing the highest
            level of service to our clients, and respecting each other.
          

        
	

        	
          
            II.
          

        	
          
            Overview – The Plan has two parts, one for the Chief
            Executive Officer (the “CEO Plan”) and another plan for the heads
            of the corporate or divisional areas (the “SLT Plan”). These plans
            are designed to reward the Company’s eligible executives (together
            the “Participants”) specifically for the performance of the
            Company’s business strategy.
          

        
	

        	
          
            III.
          

        	
          
            Plan Period – The Plan will be effective from
            January 1st, until December 31st, (the “Plan Period”).
          

        
	

        	
          
            IV.
          

        	
          
            Plan Eligibility – In order to be considered
            eligible for an award under the Plan, a Participant must:
          

        
	

        	

        	
          
            a.
          

        	
          
            be an actively employed regular full-time or regular part-time
            employee in good standing of the Company or one of its
            subsidiaries during the Plan Period;
          

        
	

        	

        	
          
            b.
          

        	
          
            for the CEO Plan, be the Company’s named Chief Executive Officer;
          

        
	

        	

        	
          
            c.
          

        	
          
            for SLT Plan, be a Senior Vice President or Executive Vice
            President in charge of a division of the Company or with
            Company-wide responsibilities;
          

        
	

        	

        	
          
            d.
          

        	
          
            not be a participant in another stand-alone incentive plan of the
            Company or any of its subsidiaries;
          

        
	

        	

        	
          
            e.
          

        	
          
            not be on written or oral performance warning; and
          

        
	

        	

        	
          
            f.
          

        	
          
            be an actively employed regular full-time or regular part-time
            employee in good standing of the Company or one of its
            subsidiaries as of the date of the award payout (the “Award Date”).
          

        
	

        	
          
            V.
          

        	
          
            Incentive Awards –
          

        
	

        	

        	
          
            a.
          

        	
          
            CEO Plan
          

        
	

        	

        	

        	
          
            i.
          

        	
          
            Incentive compensation awards under the CEO Plan shall be
            determined by the Board of Directors, or its designated committee,
            annually.
          

        
	

        	

        	
          
            b.
          

        	
          
            SLT Plan
          

        
	

        	

        	

        	
          
            i.
          

        	
          
            Incentive compensation awards under the SLT Plan shall be
            determined by the CEO and approved by the Board of Directors, or
            its designated committee, annually.
          

        
	

        	

        	

        	
          
            ii.
          

        	
          
            All individual awards determined by the CEO shall be approved by
            the Board of Directors, or its designated committee.
          

        


    

    
      
        

        

      

      
        

        

        
          


        

      

      
        

        

      

    

    

    

    
    	
           
        	
          VI.
        	
          
            Change of Control – Participants who are terminated
            as the result of a change in control of the Company, as determined
            in the sole and absolute discretion of the Company’s Board of
            Directors, or its designated committee and, in the case of SLT
            Plan, the CEO will be eligible for payment of awards for that
            portion of the Plan Period pro-rated through the date of
            termination.
          

        
	

        	
          VII.
        	
          
            Death – If a Participant’s employment is terminated
            by reason of death that Participant shall cease to be a
            Participant in the Plan as of the date of death, but will remain
            eligible for payment of an award pro rated for time of his or her
            participation in the Plan prior to point of death. The award will
            be paid to the Participant’s estate or other legally designated
            beneficiary.
          

        
	

        	
          VIII.
        	
          
            Disability/Retirement – If a Participant’s
            employment is terminated by reason of disability or retirement, he
            or she shall cease to be a Participant in the Plan on the
            effective date of such disability or retirement, but will remain
            eligible for payment of an award pro rated for the time of his or
            her participation in the Plan prior to point of disability or
            retirement.
          

        
	

        	
          IX.
        	
          
            New Hires/Transfers In – An employee becomes a
            Participant upon being hired or transferred into a Plan-eligible
            position during the Plan Period and qualifies for payment of an
            award. The Participant is eligible for payment of an award
            pro-rated for their time in the Plan starting at the point of
            hire/transfer in to the end of the Quarter in which the change
            took place.
          

        
	

        	
          X.
        	
          
            Promotions/Other Changes in Positions (to Ineligible
            Positions) – A Participant whose position changes (lateral
            transfer, demotion, etc.) within the Company to a position
            ineligible for participation in the Plan during the Plan Period
            shall cease to be a Participant in the Plan on the effective date
            of such promotion/change in position, but will remain eligible for
            payment of an award pro-rated for the Participant’s time in the
            Plan prior to the point of the promotion/change in position.
          

        
	

        	
          XI.
        	
          
            Promotions/Other Changes in Positions (to Eligible
            Positions) – A Participant whose position changes (lateral
            transfer, demotion, etc.) within the Company to a position
            eligible for participation in the Plan during the Plan Period
            shall be a Participant in the Plan on the effective date of such
            promotion/change in position. That Participant will remain
            eligible for payment of an award with the pool funded at his or
            her current funding target levels.
          

        
	

        	
          XII.
        	
          
            Termination – If a Participant voluntarily or
            involuntarily terminates his or her employment with the Company
            prior to the Award Date, he or she shall forfeit any unpaid awards.
          

        
	

        	
          XIII.
        	
          
            Funding
          

        
	

        	

        	
          a.
        	
          
            Overall Plan Funding – The Plan begins to fund as the
            Company starts to attain its threshold Company corporate scorecard
            targets. The Plan funds fully upon achievement of the Company’s
            corporate scorecard targets. The funding of the Plan may be
            increased or decreased based on Company performance as determined
            by the Board of Directors, or its designated committee.
          

        


    

    
      
        

        

      

      
        

        

        
          


        

      

      
        

        

      

    

    
    	
           
        	

        	

        	

        
	

        	
          XIV.
        	
          
            Legal Statement
          

        
	

        	

        	
          a.
        	
          
            Employment and Governing Law – The Plan is subject to the
            laws of the Commonwealth of Massachusetts and does not imply any
            form of continued employment.
          

        
	

        	

        	
          b.
        	
          
            Amending the Plan – This Plan may be subject to change in
            part or in whole without notice at the discretion of the Company’s
            Board of Directors, or its designated committee (the “Plan
            Administrator”). The Plan Administrator reserve the right to
            terminate the Plan at any time without notice.
          

        
	

        	

        	
          c.
        	
          
            Tax Withholding – No part of any award shall be required to
            be delivered until the applicable Participant (or, if that
            Participant is deceased, his or her estate or legally appointed
            beneficiary) has had the full amount of required tax withholding
            due in connection with such award delivery withheld or has made
            other provisions satisfactory to the Company for the required tax
            withholding due in connection with such award delivery.
          

        
	

        	

        	
          d.
        	
          
            Benefits – The award amounts may not be counted as part of
            any pension, retirement, or benefits plan unless specifically
            stated within the plan document of that particular pension,
            retirement, or benefits plan.
          

        


    

    
      (This Plan Document is effective 1/1/09 and supersedes any prior annual
      incentive plan document)