"I send you a cipher to be used between us, which will give you some trouble to understand, but, once understood, is the easiest to use." Jefferson wrote United State Minister to France Robert R. Livingston in 1802. Jefferson had used ciphers before with official as well as unofficial correspondence; letters to James Madison, John Adams, James Monroe, Robert Livingston, among others include communication in cipher. It was a way to keep "matters merely personal to ourselves" as well as a way to "have at hand a mask for whatever may need it."

Cognizant of the diplomatically sensitive situation Meriwether Lewis would be in while exploring the northwest, Jefferson prepared a cipher for use during the expedition and sent it to Lewis while he was preparing for the journey in Pennsylvania with astronomer, mathematician, and surveyor Andrew Ellicott.

The cipher, derived from the Vigenere cipher (that was widely used in Europe and was considered unbreakable until the 1830s), was a twenty-eight-column alphanumeric table. The correspondent would write the first line to be ciphered and then write out a keyword above, repeating it for the length of line (for Jefferson and Lewis the keyword was to be "artichokes"). The correspondent would use the up-and-down letter pairs to determine the coded letters, almost as if plotting points on a graph. Knowing the keyword the recipient could then translate the seemingly unintelligible message.

When sending the cipher to Lewis, Jefferson wrote out the instructions, "suppose the keyword to be 'antipodes' write it thus.

 a n t i p o d e s a n t i p o d e s a n t i p o d e s t h e m a n w h o s e m i n d o n v i r t u e b e n t u v y v q b & m g t s f r c s s s n j e m c u q i t m

then copy out the ciphered line thus. uvyvqb&mgtsfrcsssnjemcuqitm." Jefferson then described the method, "look for the t. in the 1st vertical column, & a in the 1st horizontal one gives u."

 a b c d e f g h i j k l m n o p q r s t u v w x y z a b c d e f g h i j k l m n o p q r s t u v w x y z & 1 b c d e f g h i j k l m n o p q r s t u v w x y z & a 2 c d e f g h i j k l m n o p q r s t u v w x y z & a b 3 d e f g h i j k l m n o p q r s t u v w x y z & a b c 4 e f g h i j k l m n o p q r s t u v w x y z & a b c d 5 f g h i j k l m n o p q r s t u v w x y z & a b c d e 6 g h i j k l m n o p q r s t u v w x y z & a b c d e f 7 h i j k l m n o p q r s t u v w x y z & a b c d e f g 8 i j k l m n o p q r s t u v w x y z & a b c d e f g h 9 j k l m n o p q r s t u v w x y z & a b c d e f g h i 0 k l m n o p q r s t u v w x y z & a b c d e f g h i j l m n o p q r s t u v w x y z & a b c d e f g h i j k m n o p q r s t u v w x y z & a b c d e f g h i j k l n o p q r s t u v w x y z & a b c d e f g h i j k l m o p q r s t u v w x y z & a b c d e f g h i j k l m n p q r s t u v w x y z & a b c d e f g h i j k l m n o q r s t u v w x y z & a b c d e f g h i j k l m n o p r s t u v w x y z & a b c d e f g h i j k l m n o p q s t u v w x y z & a b c d e f g h i j k l m n o p q r t u v w x y z & a b c d e f g h i j k l m n o p q r s u v w x y z & a b c d e f g h i j k l m n o p q r s t v w x y z & a b c d e f g h i j k l m n o p q r s t u w x y z & a b c d e f g h i j k l m n o p q r s t u v x y z & a b c d e f g h i j k l m n o p q r s t u v w y z & a b c d e f g h i j k l m n o p q r s t u v w x z & a b c d e f g h i j k l m n o p q r s t u v w x y & a b c d e f g h i j k l m n o p q r s t u v w x y z

That is, use the letter you want to change and the letter above it in the keyword to plot the coded letter. For example, the first letter from Jefferson's example message is "t" and the first letter of the keyword is "a". With your left hand, locate the "t" the first column, and with your right hand, locate the "a" in the first row. Draw your fingers together down the column and along the row to get the coded letter "u." Write that underneath the "t" and move on to the next set of letters.

Deciphering is nearly the reverse. As an example find the second letter of the keyword, "n", in the top row. Then draw your finger down the column until you find the second cipher letter, which is "v" in this example. Then draw your finger left across this row to the first column to find the letter "h."

In another example (in which the key letters are read from the bottom row) Jefferson envisioned Lewis's first message to him:

"I am at the head of the Missouri. All is well, and the Indians so far friendly."

Or more securely (with the keyword of "artichoke"):

"jsfjwawpmfsxxiawprjjlxxzpwqxweudusdmf&gmlibexpxu&izxpsecr"

Lewis recognized the need for secrecy and said that gathering information was an undertaking best approached by "stealth." However, during the journey he never found the need to use the cipher.