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In the US, all IFR aircraft need a clearance to be in class A, B, C, D, and E airspace. Does this mean that all aircraft with clearances need to be assigned squawk codes by ATC when they enter?

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No.

/X (VOR only), /D (VOR/DME only), /Y (LORAN only), and /M (TACAN only) aircraft do not have transponders. Primary-only aircraft can be assigned flight plans, and fly IFR. It's not common, though, because aircraft that will fly within 30 miles of class B airspace, or aircraft that will operate above 10,000 feet MSL are required to be equipped with transponders and Mode C altitude reporting, similar to the ADS-B requirements. (14 CFR § 91.215)

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    $\begingroup$ One downside of not having a transponder is that ATC will most likely require that you report at all the mandatory reporting points—and most pilots only vaguely remember how from studying for their IFR rating. I did have the transponder fail when doing practice approaches for my IFR. ATC had us do some turns, identified us on their scope, and then everything was like normal. $\endgroup$
    – JScarry
    May 10 at 2:19
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    $\begingroup$ What are D, M, Y and X aircraft? $\endgroup$
    – pcfreakxx
    May 10 at 13:25
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    $\begingroup$ @pcfreakxx When you file a flight plan, you need to indicate what type of navigation equipment and transponder you have on board by appending a suffix to the aircraft type, for instance, "C172/X" would be a Cessna 172 Skyhawk with no navigation equipment at all. Here is a list of all the codes. $\endgroup$ May 10 at 14:14
  • $\begingroup$ @HiddenWindshield I understand, you are talking about equipment codes. You may want to edit your answer for clarity 😉 $\endgroup$
    – pcfreakxx
    May 10 at 14:18
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    $\begingroup$ @JScarry, in 2011 (not long before I retired) I had a non-radar aircraft come on my frquency, with this - "Denver Center, N12345 (not his real name) one-five miles west of Crazy Woman V-O-R, at one-tree-thousand, estimating Crazy Woman at one-eight-fower-tree, Gillette next." I was impressed. $\endgroup$
    – atc_ceedee
    May 11 at 16:42
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Yes. Every aircraft needs to be assigne a discrete code to allow radar systems to correlate flight plan data with the radar target and to enable identification using SSR.

The only exemption are aircraft which use Mode S, those can be assigned squawk 1000 and this leads to a correlation of flight plan data using the callsign transmited by the transponder instead of the squawk itself.

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