The cytoplasmic ribosomal RNA (rRNA) genes of the Apicomplexan protozoan parasite Cryptosporidium parvum have been analyzed with respect to size, copy number, organization and structure. The small and large subunit rRNAs are 1.7 and 3.6 kb, respectively. A 151 bp putative 5.8S rRNA gene was identified. The rDNA unit is 5' small subunit rRNA internal transcribed spacer 1-5.8S rRNA-internal transcribed spacer 2-large subunit rRNA 3'. There are five copies of the rDNA unit per haploid genome and they are not organized in a conventional head to tail tandem array with a conserved external transcribed spacer. The rDNA units are dispersed through the genome to at least three chromosomes. At least two of the rDNA units are single unlinked copies on different chromosomes. There are two structurally distinct types of rDNA unit, Type A and B, with marked differences in the internal transcribed spacer regions. There are four copies of the Type A rDNA unit and one copy of the Type B rDNA unit.