Flutes require regular cleaning to keep them in good playing condition.  Proper case can help extend the life of flute pads and maintain the instrument’s sound quality.  It is good to remove the moisture from the tube of the flute, as well as under the pads, after every practice session.  
Current Flute World Ambassador Code:  ALLISON2025  for 10% off.

• Woodwind Instrument Cleaning Rod ($2.10 on Amazon) Your flute should have come with a plastic, metal, or wood cleaning rod.  That, along with a soft cloth (without frayed ends) will be enough to clean the inner tube.  Should you need a replacement, this will do just fine.

• Key Leaves Spit Sponge 2-piece ($5.99 on Amazon) are a great product to gently dab under the pads to remove excess water build-up.  These are washable for recuse, and come in a two-pack in case one gets lost or worn out.
• Hodge Silk Flute Swab ($13.50 on Amazon) are absorbent cloths to clean and dry the inside of your flute as well as polish off fingerprints from its surface.  The triangular shape reduces bulk to help swab the flute with less concern the cloth will get stuck inside your flute (it happens, and usually at the worst time). It pairs well with the cleaning rod listed above. 
• Altieri Piccolo Wand ($45.50 at Flute World) is one of the industry's most loved cleaning products - it provides the fastest and most efficient way to dry the inside of a piccolo!  *Use Ambassador Code for discount
• Altieri Flute Helix Wand ($48.50 at Flute World) is a super-swab that will completely dry the inside of the flute with one swipe!  It's easy to wash with dish soap to keep clean for years of use.  *Use Ambassador Code for discount

Please do NOT get any sort of cork grease for flutes.  Please do NOT get fuzzy cleaning sticks.
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How to clean your flute video demonstration.