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I noticed yesterday that the new eleventh edition of Merriam-Webster's Collegiate Dictionary (93) gives Down syndrome as the spelling of the main entry; within the entry, Down's syndrome is given as an alternative. The tenth edition did the opposite: it gave Down's syndrome first, with Down syndrome as an alternative.

Here is how some other dictionaries do it:
Down's syndrome only
Collins English Dictionary (British, 2000)
Encarta World English Dictionary (British paper edition, 1999)
Longman Advanced American Dictionary (American, 2001)
Longman Dictionary of Contemporary English (British, 1995)
New Oxford Dictionary of English (British, 1998)
New Penguin English Dictionary (British, 2000)
Oxford Advanced Learner's Dictionary (British, 2000)

Down syndrome only
Macmillan English Dictionary (American, 2002)

Down's syndrome as main entry, with additional reference to Down syndrome
Collins Cobuild English Dictionary for Advanced Learners (British, 2001)
Merriam Webster's Collegiate Dictionary, 10th edition (American, 1993)
Shorter Oxford Dictionary (British, 2002)

Down syndrome as main entry, with additional reference to Down's syndrome
American Heritage Dictionary (American, 2000)
Encarta World English Dictionary (American online edition, 2003)
Macquarie Dictionary (Australian, 1999)
Merriam-Webster's Collegiate Dictionary, 11th edition (American, 2003)
New Oxford American Dictionary (American, 2001)
Random House Webster's College Dictionary (American, 1999)
Webster's New World College Dictionary (American, 1999)
To explain these differences, I take the liberty of quoting at length from this page of Len Leshin, MD, FAAP:
's?

Many medical conditions and diseases have been named after a person; this type of name is called an eponym. There has been a long-standing debate in the scientific community over whether or not to add the possessive form to the names of eponyms. For quite a long time, there was no established rule as to which to use, but general usage decided which form is acceptable. So you saw both possessive and non-possessive names in use.

In 1974, a conference at the US National Institute of Health attempted to make a standard set of rules regarding the naming of diseases and conditions. This report, printed in the journal Lancet, stated: "The possessive form of an eponym should be discontinued, since the author neither had nor owned the disorder."(7) Since that time, the name has traditionally been called "Down syndrome" in North America (note that "syndrome" isn't capitalized). However, the change has taken longer to occur in Great Britain and other parts of Europe, for reasons that aren't quite clear to me.

7. Lancet, 1974, i:798.

(August 13, 2003)