Fibroblast growth factor (FGF) homologous factors-1, -2, -3, and -4 (FHFs 1-4; also referred to as FGFs 11-14) comprise a separate branch of the FGF family and have been implicated in the development of the nervous system and limbs. We report here the characterization of multiple isoforms of FHF-1, -2, -3, and -4 which are generated through the use of alternative start sites of transcription and splicing of one or more of a series of alternative 5'-exons. Several isoforms show different subcellular distributions when expressed in transfected tissue culture cells, and the corresponding differentially spliced transcripts show distinct expression patterns in developing and adult mouse tissues. Together with the evolutionary conservation of the FHF isoforms among human, mouse, and chicken, these data indicate that alternative promoter use and differential splicing are important regulatory processes in controlling the activities of this subfamily of FGFs.