I think the number of unique entries was upped to 10,000 in xl2007.

But you can't change the internal workings of excel.

But you could do a workaround like Debra Dalgleish shares:
http://contextures.com/xlautofilter02.html#Limits

JohnG wrote:

I have a large database in Excel (40,000+ rows).
When using the drop down filter button, it appears that only the top 1000
selections appear in the selection list box. This caused me to make a number
of incorrect decisions before I realised the limitation existed.
a) Is there any way to remove this restriction or to increase it to say 2000
b) Surely when this limit is reached, a warning message should appear as the
autofilter function becomes misleading.

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JohnG

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Dave Peterson