These particular tunnels were originally limestone quarries - some dating back to Roman occupation (of what was then Lutece). During the late 1700s, there were severe problems with overflowing graveyards and poor burials - especially in the region of Les Halles (once a famous marketplace, now a tragically designed commercial district). To combat the disease caused by these unsanitary conditions (becoming even more problematic during the revolution), it was decided to transfer the bodies to the former quarry sites and create mass graves.
There's something very anonymous about this sort of experience. Graveyards at least give you an indication of who each person was, but here I found myself wondering, as I looked at the rows and rows of skulls, who they were, how they lived, how they died. Though it's sure that these old bones get no rest with all us tourists wandering through day after day.