Given the potential applications of fluorescent carbon nanoparticles in biomedicine, the relationship between their chemical structure, optical properties and biocompatibility has to be investigated in detail. In this work, different types of fluorescent carbon nanoparticles are synthesized by acid treatment, sonochemical treatment, electrochemical cleavage and polycondensation. The particle size ranges from 1 to 6 nm, depending on the synthesis method. Nanoparticles that were prepared by acid or sonochemical treatments from graphite keep a crystalline core and can be classified as graphene quantum dots. The electrochemically produced nanoparticles do not clearly show the graphene core, but it is made of heterogeneous aromatic structures with limited size. The polycondensation nanoparticles do not have CC double bonds. The type of functional groups on the carbon backbone and the optical properties, both absorbance and photoluminescence, strongly depend on the nanoparticle origin. The selected types of nanoparticles are compatible with human intestinal cells, while three of them also show activity against colon cancer cells. The widely different properties of the nanoparticle types need to be considered for their use as diagnosis markers and therapeutic vehicles, specifically in the digestive system.