Normal brain function depends on an interplay between glutamatergic and GABAergic synaptic transmission, yet questions remain about the biophysical differences between these two classes of synapse. By taking advantage of a simple culture system, we present here a detailed comparison of excitatory and inhibitory neurotransmission under identical conditions using the variance-mean (V-M) method of quantal analysis. First, we validate V-M analysis for glutamatergic autapses formed by isolated hippocampal pyramidal neurons in culture, confirming that the analysis accurately predicts the quantal amplitude (Q). We also show that V-M analysis is only weakly sensitive to intersite and intrasite quantal variance and to the known inhomogeneities in release probability (P r ). Next, by repeating the experiments with GABAergic autapses, we confirm that V-M analysis provides an accurate account of inhibitory neurotransmission in this system. Mean P r , provided by V-M analysis, shows a dependence on extracellular Ca 2ϩ concentration that is nearly identical for both excitatory and inhibitory autapses. Finally, the V-M method allows us to compare the locus of short-term synaptic plasticity at these connections. Glutamatergic autapses exhibit paired-pulse depression that depends mainly on changes in P r , whereas depression at GABAergic autapses appears to depend primarily on changes in the number of release sites. We conclude that, apart from differences in the mechanisms of short-term plasticity, the basic quantal properties of excitatory and inhibitory connections in this hippocampal system are remarkably similar.