Eukaryotic circadian clocks are comprised of interlocked autoregulatory feedback loops that control gene expression at the levels of transcription and translation. The filamentous fungus Neurospora crassa is an excellent model for the complex molecular network of regulatory mechanisms that are common to all eukaryotes. At the heart of the network, posttranslational regulation and functions of the core clock elements are of major interest. This chapter discusses the methods used currently to study the regulation of clock molecules in Neurospora. The methods range from assays of gene expression to phosphorylation, nuclear localization, and DNA binding of clock proteins.