We show how a non-autonomous dynamics approach using time-resolved analyses of power spectra and phase coherence can help in the noninvasive diagnosis of malaria. The work is based on studying oscillations in blood flow and the variability of the heart and respiratory frequencies. The model used assumes that the heart and respiration are two oscillatory pumps with variable frequencies and that the vascular resistance also changes in an oscillatory manner. Red blood cells circulating through the system deliver oxygen to each cell. Malaria changes the red blood cells so that this delivery is compromised. The oscillatory properties of both pumps are also affected. We quantify the latter and compare three groups of subjects: febrile malaria patients (37); non-febrile malaria patients (10); and healthy controls (51). For each subject, time series of skin blood flow, respiratory effort, cardiac activity (ECG) and skin temperature were recorded simultaneously over an interval of 30 minutes. The oscillatory components within the range 0.005–2 Hz were analysed and their degree of coordination throughout the cardiovascular system was assessed by wavelet phase coherence analysis. It is shown that malaria, either febrile or non-febrile, substantially reduces the coordination.