Research and development projects have shown the need for strengthening hospital management information systems (HMIS) [1][2], but this has proven a difficult task, especially in developing countries [3][4][5]. The hospitals in Zanzibar have experienced problems in collecting and managing health care data due to fragmented structures and lack of standardisation. This paper analyses an on-going participatory design effort involving computer experts, health workers and hospital mangers in joint development of an integrated health information system the hospitals in Zanzibar. The challenges encountered during the process were related to the negotiation of standardised data collection, the busy schedule of health workers hampering a participatory process, the low level of computer knowledge among the health workers, the difficulties of getting correct data from the lower level’s register books, and the continuous process of establishing a culture of information use. Key lessons learned from this case study are the need to provide sufficient time to implement HIS in this context due to the difficulty of health workers and mangers to understand the logics of a computerised information system, which is needed to take full advantage of the technology. A long-term mutual training process where technical and medical/managerial personnel work together on improving information use is proposed to overcome this challenge.