Cryptosporidium infections are problematic for humans and animals, resulting in suffering and high costs for society. As symptoms are similar to other enterotoxic pathogens, specific and fast identification of Cryptosporidium oocysts is important for using the correct disinfection method and to ordinate the most suitable therapeutic. To assess if normal Raman spectroscopy is suitable to fingerprint oocysts and if their spectra can easily be discriminated from other common enterotoxic pathogens, we measured Raman spectra of single C. parvum oocysts using an LTRS instrument. Our results show that spectra of C. parvum oocysts are indeed different than those of V. cholerae and E. coli cells, as well as B. cereus and C. difficile spores. The Raman signals of viable and formalin neutralized oocysts were however largely similar. We also carried out peak assignment of oocysts and identified phosphatidylcholine as one of the major contributors to the Raman spectrum. Our Raman mapping shows that phosphatidylcholine is distributed throughout the oocyst apart from the walls, while amino acid-associated peaks are more localised, to a part of any given oocyst, which we believe is the location of the sporozoites. Thus, we conclude that Raman spectroscopy can be used to detect the presence of oocysts in water and that the unique oocysts fingerprint can easily be differentiated from other common gastrointestinal pathogens.