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This paper offers a descriptive analysis of the morphology of transitive verbs in Shilluk. Shilluk is a language in which stem-internal changes, many of them suprasegmental in nature, play an important role in the morphology, alongside affixal markers. In particular, tone, vowel length, Advanced Tongue Root (ATR), vowel height, and the stem-final consonant are involved in the morphological marking of a range inflections, expressing tense-aspect-modality, valency changes, agreement, and focus. The paper lays out the inflectional marking of these operations, for each of seven classes that can be distinguished among transitive verbs. In this way, the study extends our understanding of stem-internal morphology and its development in West Nilotic languages.