From the clinical point of view recognizing the concentrations and type profile of isoforms could be of significant practical importance. The aim of the study is designed QRT-PCR reaction to assess profile of mRNA ER-alpha and their isoforms. Theoretical part of the study was made according to computer program and available Genbank database. To detect a isoform one of the primer was designed to hybridize within exon-border linked in alternative splicing. The study presents the differentiation strategies in isoforms coming about as the alternative splicing result. Designed oligonucleotide probes and primers allow to distinguish mRNA isoforms of ER-alpha and their quantification in assessed tissues.