Animals are commonly considered to be potential sources for Giardia lamblia infections in humans, but the extent of zoonotic transmission of G. lamblia remains controversial because of inadequate understanding of its epidemiology. A better understanding of the epidemiology of G. lamblia may be facilitated by a more effective means for classifying G. lamblia isolates. To develop a sequence-based classification system, the gene encoding the metabolic enzyme triose phosphate isomerase (tim) was sequenced from a number of G. lamblia isolates of various host origins. Restriction enzymes were identified that can distinguish among isolates without the need for sequencing, simplifying the application of this approach to the epidemiologic investigation of giardiasis. Isolates from a previously reported epidemic of giardiasis were accurately classified by this technique, further verifying its utility for epidemiologic investigation.