The inherited diseases hyperkalemic periodic paralysis and paramyotonia congenita are caused by mutations in the adult skeletal muscle sodium channel gene. To determine if differences in the expression patterns of the adult and cardiac/fetal sodium channel genes could explain some clinical features of these disorders, we developed a novel mRNA quantitation strategy called quantitative multiplex fluorescent polymerase chain reaction (QMF-PCR). This assay tests the relative levels of multiple mRNA species simultaneously using automated sequenators. We show validation of this method by competitive-PCR and RNase protection. Developmental studies of sodium channel mRNAs in humans and mice by QMF-PCR showed that the adult sodium channel mRNA quickly increased, while the cardiac/fetal sodium channel mRNA slowly decreased similarly in both limb and diaphragm muscle. We find that the adult sodium channel gene expression is predominant in fetal and neonatal muscle of both humans and mice: adult isoform mRNA concentration in fetal muscle was 8.4 x 10(-6) micrograms/micrograms of total RNA; cardiac/fetal isoform mRNA was 2.0 x 10(-6) micrograms/micrograms; and actin mRNA was 3.4 x 10(-3) micrograms/micrograms. Our results suggest that differential sodium channel gene expression correlates with age of onset of disease, but not with diaphragm involvement, in patients with hyperkalemic periodic paralysis.