There are five bottles in Skyward Sword that can be used for storing potions, fairies, and some other items. The bottles can be stored in your Adventure Pouch or the Item Check.

A Gift from the Potion Shop

 
 
 
 
 
 
 
 
 

On your first visit to the Potion Shop, speak with the shop’s owner. After explaining that you need a bottle to keep potions, she’ll give you one empty bottle for free!

 

Sealed Grounds Revitalizing Potion

 
 
 
 
 
 
 
 
 

After you speak to the Old Woman in the Sealed Grounds, find the treasure chest on the right side of the room. Inside, you’ll find a bottle of Revitalizing Potion.

 

Loftwing Medicine

 
 
 
 
 
 
 
 
 

You will receive a bottle of Fungal Spores during the “Injured Loftwing” sidequest. After you have delivered the spores, you can keep and reuse the empty bottle.

 

Fire Sanctuary

 
 
 
 
 
 
 
 
 

There is an empty bottle hidden in the Fire Sanctuary.

Zelda Universe is working on a guide for obtaining this bottle that will be published at a later date.

 

Goddess Cube

 
 
 
 
 
 
 
 
 

There is an empty bottle found inside a Goddess Cube chest.

Zelda Universe is working on a guide for obtaining this bottle that will be published at a later date.