(Smallvillw Wiki http://smallville.wikia.com/wiki/Clark_and_Lex)
Although Lex did not exactly know the entire story behind Clark's alien origins, he knew there was something odd about his friend from the moment that Clark saved him by pulling him from Elbow River following a car accident. Lex was sure his car had hit Clark, and was immediately doubtful of Clark's claim that he dove after him. Lex gave Clark the opportunity to share his secret on his own terms as their friendship grew, but often could not resist asking Clark prying questions. Clark used a temporary loss of his powers to "prove" his vulnerability. Nevertheless, Lex's curiosity was not that easily satisfied.
Lex financed Dr. Steven Hamilton's excavation of Miller's Field, where Clark's ship had landed years ago, and unearthed the key to the ship. Although Lex knew that this was of alien origin, he never connected it with Clark. Lex blackmailed Roger Nixon into investigating the car crash. However, when Nixon's investigation violated the Kents' privacy, Lex demonstrated that he was not ready to trade Nixon's secrets for the Kents' lives, and thus shot and killed him. Nevertheless, Lex continued to research Clark and even stole a vial of Clark's blood from his fiancé Dr. Helen Bryce. Lex also suspected a connection between Clark and the Kawatche Caves, causing Clark to continually deny that he could read the Kryptonian symbols.
Lex eventually witnessed Clark's superpowers while in a drug-induced psychosis, confirming his beliefs. Nevertheless, the memory was lost after intense shock treatment. Not knowing what memories had been lost, Lex became desperate to recover them, which made Clark nervous.
In 2004, Lionel sent Clark a key to a secret room in the Luthor Mansion that compiled all the information Lex had gathered on Clark over the years. Three months after the fact, Lex had the room cleared out and told Clark that he was done obsessing over him and asked for his forgiveness. Lex kept his promise and did not investigate Clark for almost a year. However, he did question Clark's immunity to an airborne toxin and took advantage of Clark's temporary amnesia to ask him questions about the caves. He again "tested" Clark and was confused that his suspicions were proved wrong when he saw a video of Clark getting burned by a security laser, a subsequent brief exchange of punches leaving Clark with a bruised and bloody lip. Nevertheless, his suspicions were re-awakened when Clark came back from the dead after being shot. Lex assumed that Clark was the fast-moving blur in a security camera photo when a LuthorCorp facility was attacked. However, Lionel prevented Lex from discovering the truth by giving Clark an alibi.
Clark and Lex's growing animosity towards each other made it unlikely that Clark would ever willingly tell Lex the truth about his origins and powers, but also invited the possibility that Lex would do anything to discover it. After Clark was injured by meteor rocks and trapped in a cave-in with Lex, Lex confronted Clark about his suspected powers. Lex admitted that he had seen a chisel bend after he stabbed Clark with it. Having survived that, Lex was confused that Clark was now injured, but Clark didn't answer.
After the sudden arrival of Clark's Kryptonian cousin Kara Kent, Lex extended his curiosity towards her as well, intending to use her to reveal Clark's secret. Eventually, Brainiac, disguised as Kara, confirmed to Lex that she was an alien, insinuating that Clark was too. Lex received confirmation of this when he visited the Arctic Circle. Having come across violent aliens in the past, Lex was convinced that Clark was on Earth to destroy it and, in order to save the world, he must kill Clark.
Lex's realization left him bitter and betrayed. He told Clark that they could have accomplished anything together and that, if Clark had trusted him, he could have helped him become a hero. Clark's fear of Lex discovering his secret proved justified, as Lex then de-powered Clark and destroyed the Fortress of Solitude with the Orb, despite this attack leaving him critically injured.