In December 2013, the U.S. Office of Civil Rights issued a guidance letter providing clarification to the participation of students with disabilities in athletics and other extracurricular activities.
See:  http://www.nsba.org/SchoolLaw/Issues/SpecialEd/OCR-response-to-NSBAs-May-21-2013-letter-seeking-clarification-re-OCR-January-2013-DCL.pdf

In its letter to Mr. Negron of the National School Boards Association, several clarifying points are made.  Most notably, it emphasizes modifications that are:

• are timely
• are reasonable
• show a good faith effort

Furthermore, it establishes that a school district must make an individual inquiry to determine if reasonable modifications would allow a student to participate in an specific activity.  The letter describes what that individual inquiry might consist of by providing some limited examples.

Very importantly, the letter encourages districts to create separate opportunities for  students for whom modifications will not permit participation but does not require such an action.

Finally, the letter creates a clear separation from IDEA stating clearly that it neither enforces IDEA or offers advice on its provisions.  This advice is clearly targeted to Section 504 requirements.

Additional advice from OCR on this topic can be found in a Dear Colleague letter from January 2013: http://www2.ed.gov/about/offices/list/ocr/letters/colleague-201301-504.pdf