We have quantified activity-dependent uptake of the fluorescent dye FM1-43 in combination with immunocytochemistry for synaptic vesicle-associated proteins (SVPs) at individual synapses in primary cultures of rat cortical neurons. We show that expression of synaptic proteins is highly variable and that the levels of synaptophysin (p38), synapsin I and sv2, but not synapsin II, correlate with the extent of FM1-43 labelling at synapses. The data indicate that SVP levels affect the uptake of FM1-43 with different efficacy (p38 > synapsin I > sv2 or synapsin II). We also found that the relative levels of SVPs vary at individual boutons of single neurons grown in isolation, which indicates that differential regulation of specific SVPs may contribute to the selective modulation of activity at synapses of the same neuron.