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These were the second most valuable rupee in Twilight Princess next to the silver rupee. Now they can be found in most stages for a maximum of 1000 points! These rupees are found in pots, barrels and sometimes skulls, so start shooting. Also, when a rupee appears it will begin floating up and down. The longer the rupee stays afloat, the fewer the points it will give you until it vanishes.

Stage Rupees Location
1-1 1 Pot on right side of Mayors house.
1-2 2 Group of skulls to right once you start. Pot off in the distance on stone pedestal.
1-3 3 Pot on left once you start. Behind tent with explosive barrel. Final corner in a skeleton behind roast.
2-1 3 One in each area behind Gorons. Just look for the pots.
2-2 3 Two found in the first four pots on the river. Third is in top pot of a group of five with a red pot in the middle.
2-3 1 In the barrel in the center of the stage.
3-1 1 Pot on right of Malo's Shop.
3-2 1 Barrel down in town center to the left.
3-3 1 Found in skull on fence post.
4-1 1 In second area in center of stage.
4-2 2 First in the melon near the start. Second in skull under/near scarecrow
4-3 3 In the pots hanging in a tunnel, one in a skeleton of a spider to the left near the start, and a third in a skull to the further and left spiders on the wall.
5-1 1 Second area in entryway.
5-2 2 first in pot on a rock, second in a group of skulls under the opposed pot not containing a rupee.
5-3 3 first building on the left in pot. Group of barrels between buildings 2 and 3 on the right. In a pot with all the explosive barrels at the end of town.
6-1 1 pot near the house at the end of the level
6-2 2 pot on top of right bridge spire near start. Group of 3 explosives after bridge.
6-3 3 behind start in a pot on the right side. Second room (with keese) in a pot to the right. Under the bridge in a pot behind the chilfo and armor.
7-1 1 Second area found in skull along right wall.
7-2 2 in pots at the base of towers.
7-3 2 hallway immediately to the right in a pot. Suit of armor in first room with lasers.
8-1 2 group of skulls beginning of part 2 of the ride (evening).
8-2 1 Found in icicle stalagmite in front of cave.
8-3 2 Pot alongside wall. Suit of armor.
F-1 1 Pot inside of barn.
F-2 2 pot in far corner to right of scarecrow. Pot on pillar to right of rubble.
F-3 0