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The 39 Clues are the substances used by Gideon Cahill to discover the secret of turning lead to gold. They are scattered over the world, some in the hands of every branch of the Cahill family. Every branch doesn't know every Clue, and tries to gain them. They are called 'clues' because the lead to the secret of alchemy, Gideon's discovery of turning lead to gold.

Clue #1: HoneyEdit

The first clue was Honey, which was kept safe by the Janus branch in the US. They brought it to Salem, where the Lucians faked that the Janus were witches to get rid of them. Thomas Jefferson stole it from Paris, and hit it in his mountain home. It can be unlocked by the Card Combo: The Founding Fathers. Card 6: Thomas Jefferson, Card 44: Salem Witches, and Card 132: Abigail Adams.

Clue #2: HydrogenEdit

The second clue was Hydrogen, which was discovered by the Ekaterina branch using their Hadron Collider in CERN on the border of Switzerland and France. The discovery was a 'breakthrough' for the Ekats. The Clue is hidden in CERN. It can be unlocked by Card 28: CERN.

Clue #3: SilverEdit

The Ekaterina branch held a book written by T.E. Lawrence in their Cairo stronghold. This book contained the ancient Ekat clue of Silver. Napoleon Bonaparte invaded Egypt looking for this clue, and found something that contained a hint, the Rosetta Stone. It was taken by Ekat's and placed in the British Museum to hide it. Agent Z broke into the Ekat stronghold and solved the puzzle, Silver.

Clue #4: PepperEdit

A Cahill hid the Clue Pepper in the Angkor temple in Cambodia, and the Madrigals marked an 'M' on the ruins to scare people off. Its card is Card #206: Angkor.

Clue #5: MercuryEdit

Rival Ekats Nikola Tesla and Thomas Edison both worked to find a lost Ekat clue, but their competitive nature got in the way. Tesla found the fifth clue, Mercury, first, and hid it in his family home in Croatia. It could be obtained by completing Mission 6, or getting cards #81: Leslie D. Mill, #98: Thomas Edison, #100: The Sabotaged Lab, #106: Nikola Tesla, and #119: Airport Security

Clue #6: WormwoodEdit

The sixth clue was a Tomas clue, that they hid at the base of their Alcatraz Lighthouse, Wormwood. Its obtained by the cards #125: George Monroe Card, #128: Alcatraz Lighthouse, and Card #135: The Ghost Town.

Clue #7: BarleyEdit

The Madrigals took a Clue, Barley, to the very remote Easter Island. The Madrigals built a stronghold in a fake moai, and hid Barley in there.

Clue #8: QuartzEdit

The Tomas placed Quartz at one of the most extreme locations on the planet, the lowest. At the very bottom of the Marina Trech there lies Quartz, a Tomas Clue.

Clue #9: Cobra VenomEdit

Ustad Ahmad Lahauri was a famed Janus architect was given the clue Cobra Venom to hide in one of his statues. He chose the Diwan-i-Khas, and marked the hiding spot with a Janus wolf. You could get the Clue by completing Mission 2 or getting Cards #8: Ophir Dupham, #12: The Taj Mahal, #17: E-Mail Code, and #21: La Ngyuen

Clue #10: MagnesiumEdit

The Tomas chose Sir John Franklin to hide the clue, Magnesium, in the North Pole. The mission was to get the clue in an unknown area that other Cahills couldn't reach. Sir John's boat got trapped in ice and everyone died. It can be obtained by completing Mission 7 or collecting Cards #147: Antarctic Bling, #155: The South Pole, #186: The Lost Expedition, Card #190: Sir John Franklin, Card #192: North Pole, and Card #195: Antarctic Arnold.

Clue #11: UraniumEdit

Marie Curie discovered that the clue eleven is Uranium, and delivered it to the Ekats on an island on the Bermuda Triangle. Ekat defenses caused approaching ships to 'vanish' to protect the Clue. It can be obtained by completing Mission 0: Agent Training, or by collecting Cards #26: Marie Curie, #29: Bermuda Triangle, and Card #58: Navigation Sense.

Clue #12: WaterEdit

Water is the 12th clue, and it was discovered by Ekat Robert Cahill Henderson in Indonesia after the eruption on a volcano caused the others to be lost. He then realized the missing clue was Water, and wrote a poem about it. The poem was found by Amy and Dan Cahill who got the clue. It can be obtained by digitizing 39 Clues: In Too Deep.

Clue #13: PhosphorusEdit

Grace Cahill was flying the 13th Clue to Anne Cahill in Scotland when she was shot down by the Ekats. The clue, Phosphorus, fell into the water. The Ekats created a submarine in the shape of the Loch Ness Monster to patrol the depths for intruders. It can be obtained by Playing Mission 1 or by collecting Cards #4: Titanic, #5: George McClain, #15: Telegram, #27: Loch Ness, and #49: Paul Addison.

Clue #14: CopperEdit

The Madrigals found the Copper was a clue, and Hope Cahill had the information put in a microchip in her arm. The information was about Copper. It can be obtained by collecting Card #60: X-Ray.

Clue #15: VinegarEdit

Hope Cahill was dedicated to the Madrigal cause even after her death. Vinegar was hidden in her gravestone, a Clue. When Amy and Dan visited her grave after they'd won the hunt, they found it, Vinegar.

Clue #16: GoldEdit

Son of Thomas Cahill, Toyotomi Hideyoshi discovered Gold, a Tomas clue and hid it in a South Korean cave along with all the swords he took form the lands he ruled. The cave was found by Amy, Dan, and Alistair Oh. It can be obtained by digitizing 39 Clues: The Sword Thief.

Clue #17: IodineEdit

This Janus clue was hidden by Mary Shelly in the first edition copy of Frankenstien given to Lord Byron, and taken by Maria Marapao to the Janus's Hollywood Stronghold. The clue can be obtained by collecting Cards #13: Frankenstein, Card #85: Keat's Grave, and Card #148: Lord Bryon's Death.

Clue #18: Iron SoluteEdit

The Lucian agent Ben Franklin was charged with hiding the clue, Iron Solute in Pairs. He hid it too well, and it was lost for centuries until Dan, Amy, and Nellie Gomez found it. It can be obtained by digitizing 39 Clues: Maze of Bones. It is needed in one quantity.

Clue #19: SilkEdit

The clue Silk was given to the Janus Qing dynasty of China. In 1924, Puyi, the last emperor gave the liquid silk to George Mallory, a Tomas, to keep refrigerated at the top of Mt. Everest. It was put at the summit, by Mallory died on the way down. Amy and Dan found the vial, and it can be obtained by digitizing 39 Clues: The Emperor's Code.

Clue #20: MyrrhEdit

The Egyptian ruler Hatepshut was given a gived of Myrrh trees, valuable things. It wasn't until later that Myrrh was revealed to be one of the 39 Clues by Dan and Amy, and Ekat one. It can be obtained by digitizing 39 Clues: Beyond the Grave.

Clue #21: MaceEdit

Legendary female pirate, Anne Bonny found a lead box containing the Madrigal clue Mace in China. The box could only be opened with symbols of all five branches. The box fell into the possession of Grace Cahill, who later donated it to a Caribbean archeological dig. It was recovered by Amy and Dan who found the symbols needed to open it.

Clue #22: BoneEdit

In Zimbabwe, there is Bone, a Tomas clue. The Clue was hidden by David Livingstone when he supposedly was looking for the source of the Nile, and he hid it in a cave behind Victoria Falls. It can be obtained by collecting these cards: Card #73: David Livingstone, Card #83: Henry Morton Stanley, Card #102: The Clue Craft 3000, Card #126: Victoria Falls, and Card #129: The Tattoos.

Clue #23: RosemaryEdit

For years the four main Cahill branches have been searching in New York's subways to find the 23rd Clue, Rosemary. Only the Madrigals know where it is. It's unlocked with Card #67: NY Subway.

Clue #24: AloeEdit

The Tomas took the 24th clue, and put it in the ground with Shaka Zulu. But when revealed there's the clue, Aloe, and diamonds. Everybody thought the diamonds were the clue, until Dan decoded a message by Churchill, revealing that Aloe was the clue. It can obtained by digitizing 39 Clues: The Viper's Nest.

Clue #25: SulfurEdit

A Janus clue hidden in Turkey, Sulfur's symbol was hidden on the top of the dome. It can obtained by collecting Cards #159: Haigha Sophia Treasure, Card #194: Sky Message, and Card #207: Haigha Sophia.

Clue #26: Calcium CarbonateEdit

A Lucian clue, Calcium Carbonate was hidden in their base at Area 51. It has been safe from prying eyes for years. It can be unlocked by collecting Cards #88: Alien Abduction, #116: Area 52, #134: Stealth Plane, and #136: X-Ray Goggles.

Clue #27: SaltEdit

In the UK lies another Clue of the Lucian branch, Salt. The Clue Salt was hidden at the Tower of London in plain sight by the Lucians. It was in the Salt Tower, until it was stolen by Grace and Beatrice Cahill on their first Madrigal mission. It can be obtained by collecting Cards #158: The Last Message, #160: Sir Walter Raleigh, #181: Tower of London, #185: The Missing Colony, and #196: Raleigh's Map.

Clue #28: TungstenEdit

In Italy is a Janus clue, Tungsten swords hidden in a bench. When the right pistol is played, the piano will explode revealing the clue, because of a protoplasm rocket launcher, a highly lethal weapon used by the Lucians (found in the Black Book of Buried Secrets). Dan and Amy found it, and you can get it by finding the 39 Clues: One False Note card pack. By the way, I am totally sexy.

Clue #29: LeadEdit

A Tomas clue hidden by Simon Bolivar in Venezuela he put it there after conquering the Spanish forces. He then arranged for it to travel with his corpse wherever it went. It can be obtained by completing Mission 5 or collecting Cards #89: Jonah's Journal, #92: Simon Bolivar, #121: The Emperor's Promise, and #122: Mateo Sanchez.

Clue #30: CocoaEdit

A Tomas clue, the Clue was hidden in Macchu Picchu in the Andes, and only few Tomas knew the city was there until 1911 when it was discovered. The Tomas control the place, and the area was created a no-fly zone by Tomas in the Peru government.

Clue #31: Serum FormulaEdit

By far the most important Clue of all, the Serum Formula was hidden on a test tube in the Madrigal stronghold. It could only be activated by the fingerprints of all the branches. The Serum Formula was destroyed when Amy destroyed the serum to save Ned Starlings life. However, Dan had memorized it, and the information is still in his head.

Clue #32: ZincEdit

Tomas Jean-Baptiste Traverneir brought back a diamond, the Traverneir Blue, containing a flaw shaped like the symbol for Zinc, a Clue. The Ekaterina stole it in a raid, and cut it up, one becoming the Hope Diamond. The piece with the Clue was kept safe in Russia until Agent Z found it.

Clue #33: PearlEdit

The Janus gave King Ludwig II the Clue Pearl to watch over. He built several castles to throw suspicion off, but an Ekat doctor called him 'mad', so he was deposed. The Ekat's killed Ludwig, but the Pearl still remains in the grotto of a castle

Clue #34: CloverEdit

The Lucians needed a place to hide Clover, on the the Clues. So they built Fort Knox, and to play off suspicion, moved the US Gold Reserves and the Magna Carta there. It was discovered by Agent Z after Chrissy Collins was nearly caught for entering the building to test the Lucian security. Agent Z broke in, and found the Clue.

Clue #35: BloodEdit

Legendary Lucian genius Gustave Eiffel built his two famous landmarks, the Statue of Liberty and the Eiffel Tower, to hide the Lucian clue Blood. The Clue was rotated between these landmarks.

Clue #36: PlatinumEdit

The Janus gave Mexican ruler Maximilian a Clue, Platinum, to hide. Benito Juarez, a Tomas, learned of this and created a revolution to overthrow Mexico's government. He became president and hid the Clue in the National Palace.

Clue #37: AmberEdit

Lucians stole the Amber Room from the Nazis, and had it rebuilt under the Church on the Blood. Along with several files of Lucian research, the Amber room contains a clock that if angled right, will reveal Amber. Amy and Dan penetrated the Black Circle that surrounded the Church to get underneath and find the Clue.

Clue #38: MintEdit

During WWII, the Lucians transported a Clue out of France for safekeeping. Josephine Baker intercepted the Clue, and hid it at a mountaintop in Morocco, where it remained for 60 years until Agent Z duped Reagan Holt into getting it for him.

Clue #39: LilyEdit

At Petra in Jordan, the Clue Lily is hidden there, growing in the city. No one but the Madrigals have made it into Petra and discovered Lily, the Clue.