Shilluk is a Western Nilotic language spoken in southern Sudan. In this study, by using an autosegmental approach, which is based on lexical phonology, the author has been able to analyze the vowel and consonant harmony systems, the tonal system, and the syllable structure of the Shilluk language. Other matters dealt with include the issue of independent representations in connection with discussion of syllable structure, and the order of levels within the lexicon.