Cryptosporidium parvum has been shown, by molecular studies, to be heterogeneous in a manner linked to the host of isolation. However, no assessment of the degree of correlation between different typing systems or of the impact of geographical variation on the observed heterogeneity has been made. In this report we describe a new marker, based on point mutations in the sequence of the dihydrofolate reductase (DHFR) gene, that employed a polymerase chain reaction/endonuclease restriction protocol. The system was first tested on three well-studied isolates (a human isolate exhibiting 'human' markers, a human isolate exhibiting 'animal' markers and an animal isolate exhibiting 'animal' markers -- no animal isolates exhibiting 'human' markers have been detected to date). The human isolate carrying human markers showed a unique DHFR sequence while both the animal isolate and the second human isolate (showing animal markers in other typing systems) showed a different sequence. The new system was used successfully to type 14 C. parvum isolates from three continents. The complete agreement of this new typing system with others described earlier and the apparent linkage of alleles at unrelated loci suggested that C. parvum might have a clonal population structure.