AMPA receptors are important excitatory neurotransmitter receptors in the brain. Trafficking of AMPA receptors in and out of synapses affects synaptic plasticity. Quantum dots have been used as fluorescent probes for tracking diffusion of AMPA receptors. However, the size of commercially available quantum dots is ∼20 nm, likely limiting their ability of accessing the synaptic cleft which is ∼30 nm. Therefore, photo-stable fluorescent probes with smaller sizes are needed. In this study, we developed a new method for coating quantum dot cores to obtain stable quantum dots with diameters about 9 nm. Currently, we have successfully made small quantum dots with different emission wavelengths (527 nm, 615 nm, 620 nm and 655 nm), and functionalized them with streptavidin. Furthermore, we tested the small quantum dots on cultured neurons and found that all of them bind to AMPA receptors with high specificity. We found that the diffusion behavior of AMPA receptors labeled with our small quantum dots is different from that with commercial quantum dots, indicating that bigger quantum dots may have hindered the AMPA receptors' accessibility to the synaptic cleft. In addition, we identified micro-domains of approximately 100 nm x 100 nm where the AMPA receptors tend to bind and diffuse within these domains.