Disparities between housing, water and sanitation policy initiatives continuously undermine the efforts of informal settlements upgrading programme of transforming living conditions of people living in informal settlements. The objective of this research project was to explore the disparities between the above mentioned policy initiatives in informal settlements upgrading with the view to develop an understanding of various elements leading to these disparities. Findings of the research indicate that there are indeed disparities between housing, water and sanitation. The disparities manifested themselves at various levels of policy. The nature of these disparities also varied according to the level at which they manifested. As a result, objectives of informal settlement upgrading programme seemed to be affected negatively by these disparities.