Over the course of the series, 15 characters have come to know that Conan Edogawa is actually Shinichi Kudo (7 of which only occur in the anime). In addition, Ran Mouri has noticed similarities between the two and Kogoro Mouri and Wataru Takagi have shown signs of doubting that Conan is just "very smart".
In their respective categories, characters are listed by the order they came to discover (or become suspicious of) Conan's identity.
Hiroshi Agasa found out that in volume 1, at the second chapter of the series. Shrunken Shinichi had to persuade Agasa that the child before him is Shinichi so that he could seek help.
Akemi Miyano (Deceased)Edit
Akemi Miyano, Ai Haibara's elder sister. Conan told her his real name as Akemi was dying.
The Kudo Couple Edit
The Kudo couple, Shinichi's parents, Yusaku and Yukiko, heard that from Dr. Agasa in volume 6, after finding the Kudo household empty.
Heiji Hattori found out this fact in volume 13, as he found Conan speaking in Heiji's voice after Heiji regained consciousness from Conan's stun gun.
Ai Haibara's deduction of that was mentioned in volume 18, after knowing Shinichi's body were never to be found and that APTX4869 had de-aged some of the guinea pigs in experiments.
Sharon Vineyard (Vermouth) Edit
Vermouth realised similarities between Shinichi (when he was young) and Conan. She also chose not to betray Shinichi to the Black Organisation, most likely because he and Ran saved her when she was disguised as a serial killer in New York.
Eisuke Hondou found out in volume 60, after finding Conan's actions towards Ran is too similar to that of a boyfriend. Also, it appears as if he knew since the first time he met Conan, as at the time he purposely fell into Conan, knocking off his glasses. Then acting as if he couldn't see, he called Conan Detective Mouri.
Kaitou Kid (Phantom Thief Kid) Edit
Kaitou Kid (also known as Phantom Thief Kid) is aware of Conan's true identity in Detective Conan: The Last Wizard of the Century; how he came to know this was not given. However, the fact has not been stated in the manga and has not been confirmed by Gosho Aoyama to be canon. At any rate, Kid is definitely aware that Conan is no mere child.
Hiroki Sawada in The Phantom of Baker Street; how he knew that was not given, though it was most likely through the DNA Query Program.
In the TV Special Lupin III vs. Detective Conan, the famous gentleman thief and his associates Jigen, Fujiko, and Goemon, through some means discover Conan's true identity and help him sneak back into Japan after traveling to the country Vespadia (Conan would've needed a passport to return home, but his passport was for Shinichi Kudo).
In the 13th movie, The Raven Chaser, Black Organization member Irish discovers Conan's secret identity. However, instead of revealing it to the Organization, he decides to use that to gain more power with the boss, because of an old grudge he has with Gin for killing Pisco, his mentor, without orders to do so. He is shot to death by Chianti before he can do anything.
Although several characters have caught on to the fact that Conan is much smarter than most children, only a few characters have questioned exactly why he is so smart. Although the F.B.I. are aware of Conan's intelligence and even talk to him like he is an adult (particularly Shuichi Akai), they do not seem to be too concerned about how he got so smart.
Kogoro was the first character to become suspicious of Conan's identity, albeit briefly. In Volume 2, he noticed that Conan was once again pointing out things he overlooked, such as that all of the photos proving the suspects alibi had clocks in them. However, he instantly loses his suspicions when Conan spills another envelope of photos for the case, deciding that "a brat is a brat" after all.
Being the person who knows Shinichi the best, Ran has on more than one occasion noticed the striking similarities between him and Conan. She first becomes suspicious during the Once-A-Month Present Threat Case and even tricks him into answering to "Shinichi", however, like her father, she is easily convinced she was wrong when he begins playing with the box of toys. In Episode 96, she sees Conan without his glasses and notices he looks exactly the same as Shinichi when he was a child. She even tries to confront him about it, but Yukiko then arrives and claims that Conan is her distant nephew. After a text message she sends to Shinichi is received on Conan's cell phone her suspicions are aroused again, but Conan uses Agasa's cell phone to call her as Shinichi and messages her his "new" cell phone number. Since then, Ran has apparently been too happy with having Shinichi's "secret number" to become suspicious of Conan.
When it seemed they would both die while disarming a bomb, Officer Takagi agreed to follow Conan's instructions in exchange for telling him who he really is. Conan agreed but said he would tell him in the afterlife. Takagi had also thought to himself that Conan was not just any normal kid prior to this, but he has not made this observation since nor has he asked Conan to explain his answer.
Shiratori has often taken notice of Conan's detective skills and how unusual they are for a kid to have. At times, he actually will take note of what Conan says. It has been hinted that he may suspect something, but has not said anything to express so. But if anything, Shiratori definitely knows Conan is not an ordinary kid. However, due to his rather cocky attitude, he usually shrugs it off to solve the case. Often times, Conan must step carefully around him (He did so especially in the third movie, though later to discover Shiratori that time was in fact Phantom Thief Kid)
- All text on this page is taken from Detective Conan World Wiki.