While it has now been well accepted that neurotrophins play an important role in synapse development and plasticity, the specific effects of each neurotrophin on different populations of neurons at different developmental stages have just begun to be worked out. Moreover, the cellular and molecular mechanisms underlying the synaptic function of neurotrophins remain poorly understood. In general, synaptic effects of neurotrophins could be divided into two categories: acute effect on synaptic transmission and plasticity occurring within seconds or minutes after cells are exposed to a neurotrophin, and long-term effect on synaptic structures and function that takes days to accomplish. In this review I have considered the previous findings on neurotrophic regulation of synapses in view of these two categories. Acute and long-term effects of neurotrophins are reexamined in detail in three model systems: the neuromuscular junction, the hippocampus and the visual cortex. Potential molecular mechanisms that mediate the acute or long-term neurotrophic regulation are discussed. Efforts are made to understand the mechanistic differences between the two effects and their relationships. Further study of these mechanisms will help us better understand how neurotrophins can achieve diverse and synapse-specific modulation.