The mammalian IlF3 and NF90 proteins, involved in several cellular functions, have common N-terminal and central sequences and specific C-terminal regions. These proteins exhibit a large heterogeneity generated by posttranscriptional and posttranslational modifications. Part of their polymorphism is due to the alternative splicing of exon 3 located just downstream of the translation initiation codon. This 39-nucleotide-long exon, not described so far, codes for an N-terminal sequence of 13 residues (ALYHHHFITRRRR) also present in rat and human IlF3 or NF90. Four mRNAs are expressed in mouse brain, two for Ilf3 and two for NF90, differing in their 3' sequence to generate the specific Ilf3 and NF90 C-terminal domains and in the presence or the absence of exon 3 to generate long and short isoforms of both proteins. By RT-PCR, no other variants were found. Combining our results and GenBank sequences, we determined the exon-intron organization of the entire mouse Ilf3 gene divided into 22 exons.