Surveillance staff are vital to the success of surveillance of infectious diseases. In this study, we interviewed staff of the Communicable Diseases Surveillance System (CDSS) in Khartoum state individually and in focus groups to assess their views about the quality of the system for the years 2005–07. The quality of CDSS was considered poor because the system was not representative as it included neither the private nor military sectors nor the important teaching hospitals. It also lacked timeliness due to poor documentation, was inflexible since it did not rapidly respond to emerging and re-emerging diseases such as SARS and avian flu in its notification lists, and it did not use the data collected to apply interventions for control and prevention of communicable diseases on a routine basis. While staff were committed to the surveillance system and felt they worked hard, they were also demotivated and in the long run this might affect their performance.