What are your favorite museeums in Brussels?

Not in Brussels, but an hour by train, St John s Hospital in Brugge, and in particular the Shrine of St Ursula. For a foretaste please see gallery.euroweb.hu/html/m/memling/4ursula/

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It depends on your interests. AutoWorld is a must for car buffs; for music lovers, the Museum of Musical Instruments is fantastic (with a fabulous view from its top floor cafe). There are temporary exhibits coming in and out...right now, there is a quite good exhibit on Pompeii...
My two favorite museums in Belgium, overall, are In Flanders Field, the WWI museum in Ieper, and the Groeninge Museum in Bruges. Both are worth repeat visits.
For a "garden museum", nothing beats the Jardins d'Annevoie, near Dinant, for their superb 18th century gardens and water features.
BTilke (Brussels)

The Horta museum. Horta was an art nouveau architect, and this is his private house. An acquaintance reported that the music museum is a must.

I second the Musical Instrument museum and the roof top cafe. Loved both.

Thank you all for your help. Returned from Brussels a few days ago. I loved the Horta Museum during a previous visit. The musical isntrument museum was fabulous and I would never have thought to visit it if I hadn't received your suggestions. So you helped make my visit more enjoyable.