Developing software for children with severe illness poses a number of design challenges. In this paper we describe participatory design methods used in the development of SISOM, a support system for children with cancer age 7-12 to help children elicit and report their symptoms/problems in a child-friendly, age-adjusted manner, and to assist clinicians at the point of care in addressing and integrating children's reported symptoms and problems in patient care. The particular design challenges in the development of a clinical support tool for seriously ill children are described, followed by the participatory design techniques we used to meet these challenges. Healthy children and children with cancer participated actively in different stages of the design process. We describe how children contributed to the graphical design of the system's interface; selection of understandable, child-friendly terms used in the system; iconic and graphical representations; and its usability. The methods applied helped us to significantly improve and adapt SISOM to children's cognitive and emotional developmental stage. Working with children as partners in the design also provided important insights into the role children can play in participatory design that may be helpful for other system developers who wish to design support applications for ill children. Children had very creative design ideas that considerably improved the software. However, system development for seriously ill children also requires psychological and pedagogical insights and design and usability expertise. This limits the role children can play as full design partners.