Recent studies indicate that chromatin has a repeating subunit structure. In an attempt to relate this organization to chromatin's role in selective gene transcription we have begun to examine the subunit structure of a specific gene. Tetrahymena pyriformis preferentially replicates the genes coding for rRNA (rDNA) during refeeding after prolonged starvation. By prelabeling cultures during exponential growth with [14C]thymidine and pulse-labeling during refeeding with [3H]thymidine, we have been able to differentially label bulk chromatin and rDNA-containing chromatin. Nuclei which contained at least 78% of their 3H label in rDNA were digested with staphylococcal nuclease, and the DNA digestion products analyzed on agarose gels. Both the kinetics of digestion and the digestion products were similar for 14C- and 3H-labeled chromatin. In order to monitor protein exchange, digestions were also performed on partially purified rDNA-containing chromatin or free rDNA in the presence of nuclei. While the chromatin had a digestion pattern like nuclei, the rDNA was afforded no protection from digestion. Our conclusion is that the chromatin containing rDNA (a repeated, extrachromosomal gene in Tetrahymena) exhibits a particulate structure very similar to that of bulk chromatin. This organization does not exist in free rDNA and is not the result of protein exchange during the nuclease digestion.