Precise determination of mRNA levels is an essential element in any investigation of complex regulatory systems. Classical methodologies such as Northern hybridization suffer from requirements for significant samples of material and also a degree of nonspecificity. Recently, quantitative techniques involving PCR amplification have been devised. We have developed and applied such procedures to the determination of prothrombin messages in skeletal muscle cells during development. In addition to its role in the blood coagulation cascade, the serine protease thrombin has been shown to participate in several signaling events in the neuromuscular system. The inactive precursor, prothrombin, primarily produced in the liver, has also been shown to be synthesized and developmentally-regulated in the brain. In skeletal muscle, thrombin is a mediator of activity-dependent polyneuronal synapse elimination (ADPSE) which occurs in early postnatal development. Recent experiments showing that thrombin is released from myotubes in culture under the influence of acetylcholine suggest that locally-synthesized prothrombin may be the source of this Hebbian synaptic interaction. We have determined that prothrombin is expressed in skeletal muscle, as the likely source of thrombin involved in ADPSE, and the current results show the quantitative expression of muscle prothrombin during this time of intense synapse remodeling.