Perfluorinated compounds (PFCs) are a group of anthropogenic chemicals containing diverse functional groups and chain lengths. They are known to be persistent and bioaccumulative explaining their worldwide environmental presence. The toxicological information on these chemicals is still incomplete and insufficient to assess their environmental impact and structure-activity relationship. In the present study, the developmental effects of PFOS (perfluorooctane sulfonate, C8), PFOA (perfluorooctanoic acid, C8), PFBS (perfluorobutane sulfonate, C4) and PFBA (perfluorobutanoic acid, C4) were evaluated in zebrafish embryos (Danio rerio). The different chain lengths and functional groups of the selected chemicals made it possible to determine the structure-activity relationship of these compounds. PFCs with longer chain lengths (C8) tend to be more toxic than PFCs with shorter chain lengths (C4). Comparison based on the functional groups of compounds with the same chain length indicates that PFCs with a sulfonate group have a larger toxic potential than the ones with a carboxyl group. Furthermore, exposure to the different PFCs resulted in some general effects, such as deformations of the tail and an uninflated swim bladder, as well as in more specific effects which might be related to the structure of the tested chemicals. Oedemas and effects on length could only be detected in 8-carbon PFCs while malformations of the head were a more specific action of the sulfonated PFCs. Effects on hatching rate and success were found in PFOA exposed embryos and heart rates were affected after exposure to PFOS, PFOA and PFBS.