Calcium (Ca(2+)) is an ion vital in regulating cellular function through a variety of mechanisms. Much of Ca(2+) signaling is mediated through the calcium-binding protein known as calmodulin (CaM). CaM is involved at multiple levels in almost all cellular processes, including apoptosis, metabolism, smooth muscle contraction, synaptic plasticity, nerve growth, inflammation and the immune response. A number of proteins help regulate these pathways through their interaction with CaM. Many of these interactions depend on the conformation of CaM, which is distinctly different when bound to Ca(2+) (Ca(2+)-CaM) as opposed to its Ca(2+)-free state (ApoCaM). While most target proteins bind Ca(2+)-CaM, certain proteins only bind to ApoCaM. Some bind CaM through their IQ-domain, including neuromodulin, neurogranin (Ng), and certain myosins. These proteins have been shown to play important roles in presynaptic function, postsynaptic function, and muscle contraction, respectively. Their ability to bind and release CaM in the absence or presence of Ca(2+) is pivotal in their function. In contrast, many proteins only bind Ca(2+)-CaM and require this binding for their activation. Examples include myosin light chain kinase, Ca(2+)/CaM-dependent kinases (CaMKs) and phosphatases (e.g. calcineurin), and spectrin kinase, which have a variety of direct and downstream effects. The effects of these proteins on cellular function are often dependent on their ability to bind to CaM in a Ca(2+)-dependent manner. For example, we tested the relevance of Ng-CaM binding in synaptic function and how different mutations affect this binding. We generated a GFP-tagged Ng construct with specific mutations in the IQ-domain that would change the ability of Ng to bind CaM in a Ca(2+)-dependent manner. The study of these different mutations gave us great insight into important processes involved in synaptic function. However, in such studies, it is essential to demonstrate that the mutated proteins have the expected altered binding to CaM. Here, we present a method for testing the ability of proteins to bind to CaM in the presence or absence of Ca(2+), using CaMKII and Ng as examples. This method is a form of affinity chromatography referred to as a CaM pull-down assay. It uses CaM-Sepharose beads to test proteins that bind to CaM and the influence of Ca(2+) on this binding. It is considerably more time efficient and requires less protein relative to column chromatography and other assays. Altogether, this provides a valuable tool to explore Ca(2+)/CaM signaling and proteins that interact with CaM.