Over the last decade, epigenetic gene regulation has garnered much attention. One of the important discoveries from these studies has been that neural cells have different epigenetic landscapes from each other as well as compared to peripheral tissue. For example, in neurons the so-called sixth base, 5-hydroxymethylcytosine (5hmC) and DNA methylation outside of a CpG context (CpH methylation), is much more common than in other cells. These unique features of neural cell epigenetic mechanisms underscore the importance for examining how various stimuli and developmental programs affect epigenetic marks in brain cells, outside of whole-body physiology, and in isolation from other neural cells. In this book chapter, we describe epigenetic mechanisms, primarily histone modifications and DNA methylation, and indicate the unique aspects of studying these molecular mechanisms in neural cells. We describe methods for performing primary neuron and primary astrocyte cultures from rodents. We also provide methods for measuring DNA methylation (methylated DNA immunoprecipitation) and histone modifications (chromatin immunoprecipitation). Studies utilizing these methods have resulted in important scientific discoveries and continue to be relevant models moving forward.