Despite a multitude of commercially available multi-electrode array (MEA) systems that are each capable of rapid data acquisition from cultured neurons or slice cultures, there is a general lack of available analysis tools. These analysis gaps restrict the efficient extraction of meaningful physiological features from data sets, and limit interpretation of how experimental manipulations modify neural network activity. Here, we present the development of a user-friendly, publicly-available software called MEAnalyzer. This software contains several spike train analysis methods including relevant statistical calculations, periodicity analysis, functional connectivity analysis, and advanced data visualizations in a user-friendly graphical user interface that requires no coding from the user. Widespread availability of this user friendly and mathematically advanced program will stimulate and enhance the use of MEA technologies.