Niddah, Chapter 2, Mishnah 6. Until now the chapter has been occupied with examinations and with the practical questions that arise from them. This mishnah steps back and lays out the framework that stands behind all of those halachos: the physical structure of a woman's body, and which locations make blood found there tamei and which do not. The chachomim did not describe this in medical language. They drew a picture, a small building with rooms, and taught the halachah through that picture.
The mishnah begins with the words "Moshul moshlu chachomim be'isha": to teach these halachos, the Sages set out a parable about a woman's body. Its three components are named in the phrase "hacheder vehaprosdor vehaliyah": the chamber, the corridor, and the room above. The cheder is the room set deepest inside the building. The prosdor is the hallway through which one exits that room. The aliyah sits on top of that hallway, an upper story built over the passage.
Translated into anatomy, the cheder is the uterus, the womb itself. The prosdor is the passage leading outward from it. And the aliyah is a third space that opens into that same passage from above.
Now comes the halachah. "Dam hacheder tamei": blood whose origin is the inner chamber, that is, blood from the womb itself, is tamei. This is dam niddah in the full sense, and there is nothing uncertain about it.
Then: "nimtza baprosdor, safeik tamei". If blood is discovered in the corridor, in the passage rather than inside the chamber, its origin is not visible to us. It may well have descended from the cheder, and it may have come from elsewhere. The mishnah therefore rules that it is tamei out of doubt, "lefi shechezkaso min hamakor", because the presumption attached to such blood is that it came from the makor, from the womb. We do not treat the doubt as evenly balanced; the working assumption is that blood in the passage originated in the uterus, and so it renders tamei, though its status remains a status of safeik.
The remaining element of the analogy, the aliyah, is the subject of a long discussion. In the mishnah's scheme, blood that originates in the aliyah is not the blood of niddah, since it does not come from the womb. But what exactly is this upper chamber? The Gemara takes up the question, and the Rishonim debate it as well. A number of the Rishonim understand the aliyah to be the bladder, so that blood appearing on account of a bladder infection or a similar condition would be blood whose source is not the womb at all. This identification, however, is far from settled, and it remains the subject of extensive discussion among the commentators.
Whichever identification of the aliyah one adopts, the two plain rulings of this mishnah stand unchanged. Bleeding whose source lies in the cheder carries full tumah. And when blood turns up in the prosdor, we treat it as tamei mesafeik, since we assume it made its way down from the makor.