The mammalian circadian clock in the neurons of suprachiasmatic nuclei (SCN) in the brain and in cells of peripheral tissues is driven by a self-sustained molecular oscillator, which generates rhythmic gene expression with a periodicity of about 24?h (Reppert and Weaver, 2002). This molecular oscillator is composed of interacting positive and negative transcription/translation feedback loops in which the heterodimeric transcription activator CLOCK?BMAL1 promotes the transcription of E-box containing Cryptochrome (Cry1 and Cry2) and Period (Per1 and Per2) genes, as well as clock-controlled output genes. After being synthesized in the cytoplasm, CRY and PER proteins feedback in the nucleus to inhibit the transactivation mediated by positive regulators. The mPER2 protein acts at the interphase between positive and negative feedback loops by indirectly promoting the circadian transcription of the Bmal1 gene (through RevErbalpha) (Preitner et al., 2002; Shearman et al., 2000) and by interacting with mCRY proteins (Kume et al., 1999; Yagita et al., 2002) (for a detailed review, see Reppert and Weaver, 2002). In addition to cyclic transcription of clock genes, immunohistochemical studies on SCN neurons have revealed that mCRY1, mCRY2, mPER1, and mPER2 proteins undergo near synchronous circadian patterns of nuclear abundance (Field et al., 2000). The delay of approximately 6h between the peak in clock mRNA production and maximal levels of protein expression in the nucleus is believed to originate from posttranslational modification steps involving phosphorylation, ubiquitination, and proteosomal degradation. Thus, the timing of entry, as well as the residence time of core clock proteins into the nucleus, is a critical step in maintaining the correct pace of the circadian clock. Several clock proteins have been shown to contain nuclear export signal, sequences, on top of nuclear import signals, that facilitate their cellular trafficking (Chopin-Delannoy et al., 2003; Miyazaki et al., 2001; Yagita et al., 2002). This type of dynamic intracellular movement not only regulates protein localization, but also often affects functions by determining interactive partners and protein turnover. Because most of the clock genes have been identified by genetic screening in Drosophila and by gene knockdown in mammals, the development of innovative cellular techniques is essential in learning the structure-function and regulation of the corresponding proteins. This article discusses approaches, limitations, and applicable protocols to study the regulation of cellular localization of mammalian clock proteins, with a particular focus on mammalian CRY1 and PER2 proteins.