Firstly, it is believed in Judaism that during the night as one sleeps the souls of the sleeping rise to heaven and draw renewed life and energy for the coming day. When the soul is not present in the body during these hours, the lowest soul powers are what remain- those that allow the mechanical bodily functions to continue such as the digestive and respiratory systems. The body is left with a spiritual vacuum and as a result, impure forces can cling to the body. Therefore, upon awakening we wash our hands so as to remove the remainder of these impurities.
Secondly, it is believed that G-d returns our souls to our bodies every morning. The reason the soul is returned is so as to accomplish a unique mission today. Each morning is new chance given by G-d to serve Him. In this way we are similar to the priest who is about to serve G-d in the Temple. In the same way that the priests were required to wash their hands before performing the service in the Temple, we too wash our hands before beginning our individual service of G-d today.
Lastly, during the night, the likelihood is that our hands touched places that are normally covered. After touching those areas one needs to wash his hands before one can recite the morning blessings and prayers.
There is a Hasidic custom to place a cup filled with water that is placed inside a basin by one’s bed before going to sleep so that after saying the “Modeh Ani” prayer upon awakening, one can wash one hands.
Prior to washing ones hands, one should not touch any part of the body what has openings, including the mouth, noses, eyes and ears. One should also not touch food, drink or clothing. This is due to the belief that impurity is found on one’s hands and such impurity can be passed onto other articles that one will touch or can enter the body through openings.
The various ritual washings in Judaism vary slightly. Regarding the morning ritual washing, the hands are washed in turn- first the right hand then the left- this is then repeated two more times so that all in all, each hand in washed three times.