Fecal samples were taken from 132 (103 wild and 29 domestic) aquatic birds on selected areas in Hungary from February 2008 to March 2008. Cryptosporidium oocysts and Giardia cysts were purified from the samples and were viewed via fluorescent antibody staining. Molecular detection tools, such as PCR-sequencing and Loop mediated isothermal amplification (LAMP) were used in order to determine the Cryptosporidium species and Giardia duodenalis assemblages present. All together 6 (5.8%) and 6 (5.8%) samples out of the 103 wild bird samples and 4 (13%) and 7 (24%) samples out of the 29 domestic bird samples have been found to be Cryptosporidium and G. duodenalis positive respectively. The results of this study indicate that aquatic ducks, geese, coot and cormorant can play role in the environmental dissemination of human pathogenic Giardia cysts and Cryptosporidium oocysts in Hungary. To our knowledge, this is the first description of Cryptosporidium sp. in Anser fabalis and Anser anser, furthermore Giardia sp. in Fulica atra, A. fabalis and P. carbo and the first PCR-sequence confirmed detection of C. parvum in A. platyrhynchos and F. atra, G. duodenalis Assemblage A in A. strepera and G. duodenalis Assemblage B in A. anser.