The mammalian visual system develops to perform many complex tasks that allow us to perceive the natural world. These tasks rely on a dense network of synaptic connections transporting visual information both to and within visual cortex (V1). The laminar organization and functional properties of visual cortical neurons are largely conserved across mammals, and the mouse has been adopted as a model organism to study the development of this cortical circuit. Neurons in each cortical layer must find the correct synaptic partners for the optimal receipt, transfer, and processing of information. The molecular cues guiding the development of these connections, however, are largely unknown. In this thesis, I identify and then examine the role of molecular factors important for synapse formation in layer 2/3 (L2/3) of visual cortex. L2/3 neurons are highly interconnected and fire selectively to a refined set of visual stimuli. The developmental refinement of these visual preferences has been shown to occur in the week following eye opening, corresponding with a period of intense synapse formation and dynamic gene expression in mouse V1. In Chapters II–IV, I use the TU-tagging technique to identify molecular factors enriched L2/3 neurons before and after eye opening and identify several candidate genes with potential functions in synapse formation. In Chapter V, I examine the function of cell adhesion molecules nectin-1 and nectin-3, identified here as enriched in L2/3 visual cortex at eye opening, and previously shown to interact across synaptic junctions. I focus mainly on the effect of nectin-3 (having post-synaptic localization in hippocampus) on post-synaptic dendritic spine densities in developing L2/3 cortical neurons. I show that nectin-3 knockdown further increases spine densities after eye opening, while overexpressing a full length or truncated nectin-3 protein reduces spine densities. I conclude that nectin-3 may have a role in synapse formation following eye opening, and propose a mechanism describing the effects observed. Here, I describe a unique approach for understanding how cell-type specific connections are formed in visual cortex, beginning with the spatiotemporal examination gene expression and followed by the spatiotemporal manipulation of a single gene. This dissertation includes previously published co-authored material.