The recent development of optical methods for controlling the activity of specific populations of neurons holds tremendous promise for understanding the roles of neural subtypes in local circuits, a major goal of systems neuroscience. Optogenetic tools, in combination with electrophysiology, allow identification and manipulation of specific groups of excitatory and inhibitory neurons in active neural networks in vivo in a spatially and temporally precise manner. Here, we provide a detailed description of methods for integrating optogenetics with more traditional electrophysiological approaches as a means to probe these complex interactions.