The historic ninja uniform was called a shinobi shozoko. There were a few different colors used, depending on what was needed. Black or dark blue was used for night missions when being seen would mean certain death. White was used for winter missions so they could easily blend in with the snow covered area. The other color used was a green kind of camouflage pattern so they could blend in with the forest surroundings.
Besides the typical ninja uniform, the ninja would use any type of clothing that would get them closer to the mission goal. Sometimes the ninja dressed up as priests, peasants or even samurai. Whatever the mission required, they did.
When dressed fully in the shinobi shozoko, the ninja’s flesh was completely hidden, all except for a small slit around the eyes and his hands. The tabi boots had a slit in between the big toe and the second toe. The reason for the split was to make it easier for climbing ropes and scaling walls.
The shinobi shozoko had many pockets all through it, inside and out. This was for storing all the small tools and weapons he needed, such as poison, shuriken, knives and so on. The ninja also carried a small, primitive, first aid kit, filled with potions and solutions.
The footwear the ninja wore was called tabi, or tabi boots. These boots had a split cut out between the big toe and the rest of the toes. This made climbing much easier.
Read more about the tools the ninja used here.