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While it is unknown, and unlikely, that Takagi knows Conan's identity (Shinichi), there seems to be  hints of him knowing it. Please note that the evidence to support this theory is not anime safe.


Suggestive Evidence to support that Takagi knows Conan's is Shinichi:

• Takagi knows that Conan is not a regular child.

-In Vol. 36-File 11 (Masuda Case), Takagi asked Conan who exactly he was. Conan answered by telling Takagi that he would answer 'in the afterlife'. Conan's answer implies that he is not an ordinary child, and likely not who he says he is (Edogawa Conan). Takagi has already known Conan to be a bright, intelligent child at the time, but did not question him until the two were faced with a life threatening incident. This suggests that he has either been suspicious of Conan for some time not being who he says he is, or realized that something was odd about Conan with Conan defusing the bomb.

-Takagi has great, nearly uncanny trust of Conan. Even if Conan is known to be a bright, intelligent, sharp child to the Metropolitan police, his trust in Conan seems greater than that of most other officers. In addition to listening to Conan's deductions, on some cases with the Detective Boys present, Takagi only brings Conan with him. (File 671 P.10 (Destiny's Scar)—Takagi only allows Conan out of the car to question the family members of the deceased, while the eye-witnesses, Ayumi and Haibara, are left in the car to observe the people they meet. If Takagi wanted Ayumi and Haibara to identify the culprit, would it not have been best to bring those two to meet the family members of the serial killer's victims? What is his purpose for bringing Conan to questioning, aside from hoping that Conan would be able to help?). Under Conan's request, he even posed as a postal worker in file 761.

-Takagi has witnessed Conan using his tools/gadgets. Conan used his shoes and belt from Professor Agasa to knock out a kidnapper in front of Takagi in file 761 p. 14. On the same page, Conan mentioned that he knocked the woman out using his tranquilizer watch, which implies that he knocked a culprit out using that watch in front of Takagi.

• Takagi is suddenly close enough to Shinichi to be on first name basis with Shinichi

-In File 770 P. 10 (Jeet-Kune Do), Takagi reacted to Conan's phone call as Shinichi by saying “Shinichi-kun?â€

Spoilers aren't necessary in here.

I was about to disregard the theory and say that Takagi has of course realised that Conan is extraordinarily smart for a 6 year-old, but hasn't looked into him enough to find out that he really is, especially since the truth is quite far-fetched.

But then I had another look at chapter 770 and Takagi seems genuinely distressed that Shinichi is on the phone. as if he's thinking "But Conan-kun is Shinichi-kun, how is that possible?".

Arisana wrote:

• In file 609, Conan's cell phone, which contains Conan's fingerprints, was offered as evidence to identify whether or not the corpse was Akai Shuuichi. Takagi was the officer who took the cell phone for investigation. Conan and Shinichi's fingerprints are proven to be the same in file 651, when Heiji offered a charm containing Conan's fingerprints to identify whether or not the culprit was Shinichi. It may or may not be possible for Takagi to check if Shinichi and Conan's fingerprints were identical or not, but the police does have Conan's fingerprints with them, and possibly Shinichi's.

I also find this point suspicious. Since Conan and Shinichi would have the same fingerprint, it seems weird that Takagi didn't question that regard about his fingerprint.

Finally, someone else agrees!!!  :D
I also noticed most of those things and I really, really hope that Takagi knows, it would be almost as fun as when Hattori comes along (as in: Takagi: Shi-Conan-kun! all the time). Although, if he's suspected it for a while (as it seems) then Takagi is a lot better at keeping secrets than we give him credit for.
Oh... I just realised something, y'know in file 760 Sera asks 'Shinichi' if he's in the right place and gets a reply saying basically that he's not there so he wouldn't know despite the fact that a) he shouldn't have been able to hear him from there and b) he replied and Sera heard him. If Takagi also realised what that implied then he could start to make the jump to Sleeping Kogoro (Conan would need a voicechanger of some sort to call while being in front of them + Conan's tranq watch which he's seen).
...all hypothetical of course

This might really be true o.O" *never thought about it before*

Wow, that actually makes a lot of sense. o.o Kudos to you! (lol)

Ah, I see. Thank you for letting me know that Rule 4 doesn't apply in this case, Dus. (I wasn't too sure whether it did or not, and there was a point from File 770)Fixed it now.

Hmm, yes come to think of it, it is possible that Takagi might have figured something out from the phone call. If Takagi really has figured out who Conan is, then his situation would be similar to Eisuke (Eisuke suspected it, but didn't confront Conan until the end.)

I don't think so. What I get from his reaction is this:
He more or less had it figured out and when "Shinichi called" he was all like "WTF, how is this posible? I thought Conan was Shinichi." Simply because he didn't know Conan has two mobiles and unlike Sera he hasn't seen Conan playing around with the bow-tie and his second mobile.

I agree with you about the fact that Takagi didn't know that Conan has two mobiles, but while he hasn't personally witnessed the voice changer, if he did suspect that Conan is Shinichi, he would know that Conan has some way of using Shinichi's voice through the phone. In the case with Satou's marriage arrangements, Conan had phoned him using Shinichi's voice. It's likely that he would believe that Conan had an accomplice with Shinichi's voice relaying deductions for him or had some form of machinery to allow him to imitate Shinichi's voice if he had more or less figured out the connection between Conan and Shinichi.

Also, he could figure something out after the fact as he seemed sorta shell shocked for most of the rest of the file. I doubt Aoyama would have done something so hard to do on accident unless he was implying something (I'm refering to the 'Shinichi-kun' thing that had to be a conscious decision on his part) so it's got to play a role. By that I mean that he wouldn't have an arc of suspicion for Takagi without bringing it to the front at some point, no suspense otherwise.

EDIT: Takagi could have just been stunned at Conan 'phoning Shinichi up' right in front of them. Hmm, doesn't fit as well as the other ideas though.

Yes, Takagi would have had an opportunity to look into Conan and find a connection to SHinichi for some time now, but so far there haven't been any hints that ha had, or I've missed them.

Were there any hints that Eisuke knew? If the signs are similar with Takagi then it makes it seem more plausible (random glaring doesn't count, by the way  )

In Eisuke's case, perhaps the 'It's an honor to meet you, Mouri-tantei' directed at Conan applies, then there was an immediate hint that Eisuke knew. Perhaps other hints were in the Eisuke arc, but I've missed them.

In the the arc where Vermouth was revealed to be disguised as Araide, we barely saw Conan piecing it together, and Gosho dropped hints. Until that point, it seemed more likely that Jodie was Vermouth.

Up until file 770, there didn't seem to be any hints of Takagi knowing, ignoring the Masuda Bomb incident since he didn't seem to know Conan's identity for some time after that case. It's possible that Gosho is just starting to insert Takagi's knowledge into the plot.

I never really thought about it...but this is really convincing. 
Also, with the whole fingerprint thing, shouldn't the police have Shinichi's fingerprints since he started investigating like, two years previously?  I mean, lots of times the police say, "we need your fingerprints even though we know you're not the culprit but you touched this (insert object here)..."  Wouldn't Shinichi's fingerprints be on file?  It wouldn't be hard for Takagi to get at them.
Me, I dunno if he knows he's Shinichi per se, but he's gotta know that there's a link between Shinichi and Conan.  I mean, that a 17 year old suddenly became 7 is a big leap.  But then again,  Takagi is pretty open-minded.

Stopwatch wrote: Were there any hints that Eisuke knew? If the signs are similar with Takagi then it makes it seem more plausible (random glaring doesn't count, by the way  )

I don't think there were any other noticeable hints aside from when Eisuke was introduced and he purposely fell.

And the police should be able to access Shinichi's fingerprints, but if they ever had Conan's fingerprints, something odd should've come up.