Abstract Although estrogen receptor alpha (ERα) mRNA has been detected in the primate frontal cortex, the types of ERα transcripts expressed, including exon-deleted variants (Δ), have not been determined in the monkey or human frontal cortex. Because the types of ERα mRNA expressed in brain could define neuronal responses to estrogens, we examined the transcript pool of ERα mRNAs expressed in normal adult and developing human and macaque frontal cortex. We reverse transcribed total RNA from the postmortem frontal cortex of 29 normal adult humans, 12 rhesus macaques, and 19 people ranging from infants to adults and employed two rounds of nested polymerase chain reaction (PCR) to generate ERα products spanning the coding domain. In a third nested PCR, we used primers specific for novel sequences of exon–exon junctions created when whole exons are missing. By sequencing PCR products, we detected 60 instances of 12 distinct ΔERα mRNAs in adult humans and 94 instances of 13 distinct ΔERα mRNAs in monkeys in differing patterns from one individual to another. In adult humans, 83% of individuals expressed at least 1 ΔERα mRNA variant, and 100% of the monkeys expressed at least 1 ΔERα mRNA variant. The single Δ2, Δ5, and Δ7 variants were frequently expressed in both human and monkey frontal cortex, Δ3 variants were rare in both species, and Δ6 variants were more frequently expressed in monkeys. In both species, we detected double, triple and quadruple Δs, but these were less common than single Δs. The pattern of human variant expression did not appear to change dramatically as a function of age. These findings imply the potential to produce different ERα proteins in frontal cortex, possibly with altered structure and function which may have physiological relevance for gene transcription by virtue of altered functional interactions with each other, other steroid hormone receptors, and genomic DNA.