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In the Miqraot Gedolot, an index exists called Toldot uVeit Aharon. It lists "every" passage in the early rabbinic literature that references every individual passuk, and is extremely useful. Another, more fuller, version of the same is the three-volume Torah haKetuvah vehaMesorah. Does anybody know if a similar index exists for the Mishna? I would love to be able to know where any individual mishna is referenced throughout the Bavli and the Yerushalmi.

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Mesoret hashas? – Double AA Jan 31 '13 at 14:15
Mesoret haShas is good if the Shas is your object of study, but not if your object of study is the Mishna. For that, you could use Mesoret haShas in order to compile such an index, though it would take a long time, and it would require you to go through the entire Bavli. I would rather target a particular mishna, then see everywhere in the Bavli (and Yerushalmi) that the sages refer to it. – Shimon bM Jan 31 '13 at 14:39
up vote 2 down vote accepted

There's one, with a title atop the column that reads "ציונים", in the outside margin of the standard-print mishnayos (the one with the Yachin Uvoaz).

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