Cryptochromes are blue-light photoreceptors that regulate the circadian clock in animals and growth and development in plants. Cryptochromes have high sequence homology to DNA photolyase but appear to lack photorepair activity. All previous work on cryptochromes was performed with protein expressed in heterologous systems; hence, biochemical and photochemical studies performed with these proteins were subject to certain limitations. In this study, we purified cryptochrome 2 (hCRY2) from human cells and characterized it. We find that hCRY2 exhibits fluorescence properties consistent with the presence of folate and flavin cofactors. Cryptochrome 2 binds to double-stranded DNA weakly and to single-stranded DNA with higher affinity, and this binding is further stimulated by the presence of a (6-4) photoproduct. However, light has no effect on the cryptochrome 2-(6-4) photoproduct complex. These findings reveal new properties of this protein already known to function as a circadian photoreceptor and a light-independent negative transcriptional regulator of the clock genes.