Board Thread:Naruto Discussions/@comment-26636534-20151016181609/@comment-24757127-20151021010812

Georgio722 wrote: Well, Nagato's injuries are caused by the use of Rinnegan, so maybe it's outside the healing abilities of the Reanimation Jutsu? Seems logical though.

Not his legs. His legs were crippled from Hanzo's Fire Release: Exploding Flame Manipulation. A regular jutsu. The rinnegan just fatigued him heavily because of the massive amounts of chakra the TT took and it stuck him with the chakra rods.