Sleeping sickness in east and central Africa is caused by a protozoan parasite, Trypanosoma brucei rhodesiense. About 12.3 million people are at a risk of acquiring the disease that is fatal if untreated. The disease progresses from an early stage with trypanosomes in blood and lymph to a late stage in which trypanosomes enter the central nervous system. Variations in disease presentation, progression and severity of the disease have been reported and cytokines have been proposed as potential players. Before treatment is commenced, disease stage has to be ascertained since treatment for the two stages is different. The currently used staging criteria depends on finding trypanosomes in the cerebrospinal fluids (CSF) and elevation in CSF white blood cells however, this has been found to have low sensitivity. We therefore measured plasma and cerebrospinal fluid cytokine concentrations and determined associations with disease presentation, stage progression and severity of the neurological response. Our study shows that concentrations of specific cytokines are elevated in sleeping sickness patients and have a potential to discriminate between patients in early or late stage of infection.