We observed local homology between human pendrin and sodium/iodide symporter (NIS), that was absent in the NIS-homologous sodium/monocarboxylate transporter or apical iodide transporter (AIT) which, however, does not transport iodide. Thus, we analyzed the full proteins. They shared 63 identical and 66 similar residues (overall homology 14.4%, but 21% when omitting intervening sequences of 15 or more residues). Pendrin was more homologous to NIS (25%) than AIT (20%), particularly in the STAS domain (sulfate transporter and antisigma factor antagonist). Homology was concentrated in 11 segments, with 3/11 involving the STAS domain. In 9/11, homology was greater with NIS (45-58.3%) than with AIT (8.3-42.3%); in 4 of these 9 segments, homology was comparable to or greater than that between NIS and AIT (8.3-52.6%). Pendrin residues which are mutated in Pendred's syndrome are identical to those in the aligned position of NIS and AIT. Hypothyroidism-associated pendrin mutations almost always fall within 4/11 segments. These are the first data that show homology between pendrin and NIS, and topographic relationships between pendrin mutations and the hypothyroid phenotype of PDS.