We have obtained a novel cDNA species of MKK3, termed MKK3b. MKK3b cDNA differs from its original form, MKK3, at the 5'-end, encoding 29 extra amino acids in the N-terminus. Analysis of MKK3 genomic DNA structure revealed that the MKK3b-unique 5'-end sequence is derived from an exon different from that of MKK3, and that they share identical sequences thereafter. This suggests that the two cDNA forms of MKK3 are either generated by differential splicing of the same gene or derived from differential promoter utilization. Northern blotting analysis showed that MKK3b mRNA is much more abundant than MKK3. Functional characterization based on the activation of p38 revealed that MKK3b is more efficient than MKK3 in mediating downstream signalling events.