Misao's Body Parts are necessary items the player must locate throughout the game in order to save Misao and end the curse. They must be sacrificed at the Altar located in the Abyss. In the Definitive Edition this was instead changed to six items belonging to Misao; except for her hands, which aren't referred to by name and kept covered.
There are six body parts in total.
Misao's arms are given by Mr. Sohta after performing a few tasks. He is found trapped inside the locker in Class 2-A, followed by the Infirmary with Ayaka once he is freed. After searching the Staff Room for a tranquilizer and returning empty-handed, you will find that Ayaka is dead and Sohta wounded. After speaking to Sohta, you will be given Misao's Arms.
Misao's head can be found in a minecart in the Bottom of the Well. To access the minecart, you must first go to the Science Lab and hide inside the large corpse, then wash off the blood in the Bottom of the Well.
Misao's legs can be found after finding Kudoh. After his death, returning to the Boy's Bathroom will reveal the car that ran him over has crashed through the room. Opening the car door, Aki finds her legs.
Misao's eyes can be found in a chest on the Rooftop, once the Lilles are put into the three vases found in the classrooms.
Misao's heart is locked in a capsule in the Science Lab. To unlock it, use the Boot Disk at the computer and enter in the correct code, then go to the back of the lab and enter another code into the console.
Misao's brain can be found in the locker found second from the left in the Staff Room. It is unlocked using the Small Key found after rescuing Sohta.