The Mishna Berura (Rav Yisrael Meir Kagan of Radin, 1839-1933), in Siman 4, writes (citing the Seder Olam) that upon awakening in the morning, one should not touch his garments before washing Netilat Yadayim. One should immediately proceed to Netilat Yadayim after waking, before taking off his pajamas or getting his shirt, pants, or other garments.
Rav Shlomo Zalman Auerbach (Jerusalem, 1910-1995), in Isheh Yisrael (1:23), writes that an exception may be made regarding the Kippa. Many people wear their Kippa when they go to bed, and indeed the Ben Ish Hai (Rav Yosef Haim of Baghdad, 1833-1909) writes that this is a proper practice. Of course, by the time one wakes up his Kippa is no longer on his head, and Rav Shlomo Zalman noted that the prevalent custom is to allow putting ones Kippa on his head before Netilat Yadayim in the morning. The Magen Abraham (Rav Abraham Gombiner, Poland, 1635-1682) in any event wrote that from the Gemara it appears that one may touch his clothing before washing hands, and so although we generally do not follow this view, when it comes to the Kippa we may rely on the Magen Abraham and put it one before washing.
