I  just bought a 2001 (April 2008) which was alway garaged and only has 21k miles. I really enjoy this car but I am having the same problem.  The lady I bought it from said she rarely lowered the top because the boot was too much trouble. I agree with that, but I drive mine daily and lower the top whenever weather permits (NW Fla). I assume that it is the repeated lowering and raising of the top that exacerbates the problem.  It seems from all the posts that I have seen, that this issue is quite common to the '01 model year.

The problem just arose in the last week so I have not consulted with my local Audi repair or top shop yet, but $3k seems a bit excessive to replace the entire top.  I had to replace the top on my previous car (2000 SL500) because the plastic rear window completely fogged over (one reason I swapped it for the TT) and it was only $2100 including the padded liner.

I think the idea of removing the top, regluing the seal and stiching the seal back to the top sounds like the ideal remedy but I'm sure my labor cost will be considerably higher than in the Middle East.

If I can't get a reasonable estimate for doing that or replacing the top, I'm going to try the glorilla glue route.

Will post as to outcome.

Can't speake for the glorilla glue but i used weather strip addhesive by 3M let it sit for awhile and the applied a small bead of silacone RTV on the outside let it all set over night and it worked great and you cant tell that it was done it has been a month now and the top has been up and down plenty and is doing great just another option for you..

Found a top shop that will replace the top for $1200 and waranty the job.  Decided to take this route.

Previously mikeacct wrote:

I have a 2001 TT Roadster that has been religioulsy garaged and has only 36K miles. After sitting in the florida sun, the back window separated from the cloth top. It appears as if the glue malfunctioned. The dealer tells me this is not a common problem and it would cost $3,200 to replace as the window cannot be re-attached. Even though my warranty has recently expired, I feel this is a defective situation. If I cannot get relief from Audi, I am considering a local car shop who says they can replace for $900. Has anyone had this problem or replaced the top in the secondary market?

Previously mikeacct wrote:

I have a 2001 TT Roadster that has been religioulsy garaged and has only 36K miles. After sitting in the florida sun, the back window separated from the cloth top. It appears as if the glue malfunctioned. The dealer tells me this is not a common problem and it would cost $3,200 to replace as the window cannot be re-attached. Even though my warranty has recently expired, I feel this is a defective situation. If I cannot get relief from Audi, I am considering a local car shop who says they can replace for $900. Has anyone had this problem or replaced the top in the secondary market?

Hi, I have an auto upholstery shop in Sarasota, Fl. For several years now I have been in contact with a few different research & developement people at my usual top manufacturers. Most of them still build tops using the same method used in the late 1960's to 1970's to bond the glass to the top material. They hardly ever came loose back in those years. I've worked for over 5 years trying to figure out the process used. I believe, right now, I might have it figured out where i can do it on the car. I have a TT that has been with the owner for over 3 years with my reattached rear glass still in place. I had the window on my bench to clean it before reinstalling it. Right now we have a newer beetle with the rear window loose. We've done a few of these this year. A-4s we've done. Corvette C-5s are another we've been successful with. The finished look on the outside is almost original.