Molecular heterogeneity of kainate-selective glutamate receptor subunits GluR5 and GluR6 was revealed by identification of a human cDNA, GluR5-1d, and a murine cDNA, GluR6-2, that each encode subunits with novel carboxy-terminal sequences. Both GluR5-1d and GluR6-2 appear to be generated by alternative splicing at analogous sites 14 codons following the fourth putative transmembrane segment. The principal transcripts of GluR5 and GluR6 were detected by Northern analyses of several regions of mammalian brains as 4 and 6 kb bands, respectively. Potential roles for these receptors in development are indicated by detection of their mRNAs in mouse embryos of 11 days gestation. These findings add to the description of the remarkable diversity of glutamate receptor gene expression.