Confidential Executive Transition Agreement

EXHIBIT 10.52

Confidential Executive Transition Agreement

     This Confidential Executive Transition Agreement (“Agreement”) is entered into by and between ILLUMINA, INC. (“the Company”) and JOHN R. STUELPNAGEL (“Executive”) (collectively “the Parties”), as of the date of the last Party to sign it below, with respect to the following:

     A. Executive shall work in his current role with the Company through March 31, 2008. In doing so Executive will continue through March 31, 2008 (i) to act in the same Executive Officer capacity as Executive has been holding to date, driving the operating goals and results of the Array Business Unit; (ii) to serve as a Director in the Company; and (iii) to be compensated at his current level.

     B. Effective April 1, 2008 at 12 a.m. Pacific Time, Executive shall resign his position (i) as the Company’s Senior Vice President, Chief Operating Officer and General Manager Micro Arrays, and (ii) from the Company’s Board of Directors.

     C. Effective April 1, 2008 at 12 a.m. Pacific Time, Executive’s Change in Control Severance Agreement made as of August 21, 2006 shall terminate without any additional notice or other action on the part of the Company.

     D. With the first bi-weekly pay cycle after April 1, 2008, Executive shall be paid in full his unused paid time off accrued through March 31, 2008.

     E. Commencing on April 1, 2008 and through March 30, 2009, Executive shall become an Illumina Fellow that is defined as a part-time Company employee acting in an advisory capacity to the Company’s CEO and Management.

     F. The specifics of Executive’s part-time employment with the Company shall be as follows:

	1.		“Part-time” is defined as up to 25% of a standard work week with additional time as mutually agreed between Executive and the Company CEO.
	2.		Unless otherwise mutually agreed between Executive and Company CEO, Executive will work on the development of the Infinium HD and follow-on products and their manufacturing. Executive may undertake other assignments by mutual verbal agreement between Executive and Company CEO.
	3.		Executive will work up to 25% of a standard work week on average if requested and shall be paid on an hourly basis for the time worked at an equivalent hourly rate to Executive’s current salary. Executive shall be compensated at a minimum of 5 hours worked each week, even if the actual hours worked fall below this level.

	4.		From April 1, 2008 to March 31, 2009 (12 full months), Executive shall continue vesting his existing stock options as if Executive was working as a full-time Company employee.
	5.		From April 1, 2008 to March 31, 2009 (12 full months), irrespective of time worked in any period, Executive will continue to receive Company health and welfare benefits under conditions then applicable to part-time Illumina employees, unless such benefit is prohibited by Company policy or by the Company’s group insurance policies in effect at that time. Notwithstanding the above, Executive will retain his access to the Company’s exercise facility.
	6.		From April 1, 2008 onward, Executive will neither accrue paid time off nor will Executive earn or be eligible to receive any bonus, stock option or restricted stock unit grants.
	7.		During his Part-time employ