Recent studies indicate that the Egr family of transcription regulatory factors plays a key role in nervous system development and plasticity. In prior studies, we demonstrated that multiple isoforms of the Egr3 transcription regulatory factor are expressed in brain and appear to be generated by use of alternative translation start sites. To compare the functional activity of these isoforms, we have examined their ability to stimulate transcription of a luciferase reporter construct driven by the Egr response element. Analysis of a series of N-terminal truncation constructs indicates that Egr3 contains two distinct activation domains: one located in the segment upstream of Met(106), the start site of the major truncated isoform Egr3beta, and the other located C-terminal to all of the alternative translation start sites used to generate Egr3 isoforms detected in brain. We confirmed this inference by demonstrating that each of these segments is able to drive transcription when fused to the GAL4 DNA binding domain. Taken together, these studies indicate that the internal translation start sites present in Egr3 are used to generate Egr3 isoforms lacking the activation domain located N-terminal to Met(106).