The speed and reliability of neuronal reactions are important factors for proper functioning of the nervous system. To understand how organisms use protein molecules to carry out very fast biological actions, we quantified single-molecule reaction time and its variability in synaptic transmission. From the synaptic delay of crayfish neuromuscular synapses the time for a few Ca(2+) ions to bind with their sensors in evoked neurotransmitter release was estimated. In standard crayfish saline at room temperature, the average Ca(2+) binding time was 0.12 ms for the first evoked quanta. At elevated extracellular Ca(2+) concentrations this binding time reached a limit due to saturation of Ca(2+) influx. Analysis of the synaptic delay variance at various Ca(2+) concentrations revealed that the variability of the Ca(2+)-sensor binding time is the major source of the temporal variability of synaptic transmission, and that the Ca(2+)-independent molecular reactions after Ca(2+) influx were less stochastic. The results provide insights into how organisms maximize reaction speed and reliability.