Parasitic diseases such as malaria remain a mayor burden on global health. One of the biggest challenges still to be overcome is that of inadequate diagnoses. This research explores the opportunities that Hyperspectral Imaging yields in this field. The first goal is to estimate the spectral signature of Malaria parasites in non-stained or Giemsa-stained thin smear blood samples and of Schistosoma parasite eggs in urine samples. For this different endmember extraction algorithms are combined with various methods of pre-processing and dimensionallity reduction. The used endmember extraction methods are pure pixel index (PPI), NFINDR, Statistics Based and simplex identification via split augmented Lagrangian (SISAL). For denoising Savitzky Golay and 3 dimensional gaussian filtering is used and the dimensionallity reduction is done with PCA, ICA or HySime. The resulting spectral signatures of the algorithms are validated by inspecting the endmember locations, spectra and abundance maps. They have furthermore been compared by the classification performance where the spectral signatures are used in the feature derivation. This is done by deriving a detection map using OSP or CEM detection and then using the SVM or random forest classifiers to classify cells as being infected or not. These performances are furthermore compared to RGB image based classification. In case of the stained Malaria sample the four endmember extraction methods are shown to be applicable to various degrees. Firstly, the PPI method is shown to be inconsistent, resulting in different spectra each run. Secondly, the statistics based method unable to separate the spectral signatures of the red blood cells and thirdly the background. Thirdly, The NFINDR method seems to work well considering the endmember locations, spectra and abundance maps, but leads to a low classification performance. The research concludes that Sisal made the most accurate estimations of the spectral signature of the parasite. The results from all the validation methods are in line with expectations. Furthermore, the use of this spectral signature in the feature derivation process results in the highest classification performance. This performance is also shown to be significantly higher compared to using either the first principal component of the full hyperspectral data or the RGB images. Applying the same methods to the Schistosoma sample it is found that some of the methods, though interestingly not Sisal, are able to to create an abundance map in which the egg is separated from the background. However, none of them are able to separate the egg and the white blood cell and detection maps using these signatures did not show the egg more clearly than the first principal component did. None of the methods are found to be able to extract the spectral signature of the unstained Malaria parasite. Finally, a hypothetical multispectral microscope is proposed which images at the wavelengths where the spectral signature of the parasite in a stained sample has the biggest difference in light transmittance to the other endmembers. This setup is simulated from the available hyperspectral data and its classification performance is compared to classification performance using the full hyperspectral data and using the RGB images which are simulated from the same data. The classification using the discriminative wavelengths is found to outperform both in terms of sensitivity and specificity. This implies that the images at these specific wavelengths provide more discriminative power and such a multispectral setup could provide a significant advantage over RGB imaging.