We determined species/genotype(s) of enteric microsporidia and coccidia causing diarrhea among 44 liver transplant children in Shiraz Nemazee hospital using acid-fast-trichrome staining and polymerase chain reaction-sequencing techniques. Enterocytozoon bieneusi (genotype D), Cryptosporidium (parvum and meleagridis) were detected in 6.81% and 11.36% of the children, respectively.