Abstract. A retrospective epidemiologic study was conducted to evaluate the application of an objective quantitative algorithm for estimating genetic similarity from restriction endonuclease analysis data. The analysis was performed to assist the determination of chronologic trends in an Aujeszky's disease viral epidemic in a geographic region. DNA from each viral isolate obtained during the epidemic was digested with 4 restriction endonucleases and molar ratio labeled to generate separate fragment patterns that were simultaneously compared using the algorithm. The resultant estimates of genetic similarity were then used in conjunction with time of virus isolation and specific geographic location of the outbreaks to identify the probable sources of infection and the patterns of spread among swine herds. This type of quantitative analysis enabled a more precise and objective approach than previously has been applied to the interpretation of restriction endonuclease data, thereby demonstrating the benefit of this methodology for the investigation of infectious disease outbreaks.Restriction endonuclease analysis (REA) has been used as an epidemiologic tool to support hypotheses regarding the source of Aujeszky's disease (AD, pseudorabies) virus (ADV) infection for swine farms and individual animals. 7,8,24,26,38 Restriction fragment length polymorphism (RFLP) among viral isolates has been used to distinguish field and vaccine strains of ADV. 11,12,19,29 To utilize REA for epidemiologic purposes, it was necessary to establish that ADV is relatively stable genetically, both in vivo and in vitro. In previous study, there was enough viral genomic stability in a swine herd to enable the use of REA to categorize isolates into strains. 10 This type of first-order molecular characterization of DNA polymorphism has been based on visual comparisons and/or the use of 1-dimensional computerized dendrograms to produce phylogenetic trees representing the percentage of similarity or diversity.Considerations of an ADV epidemic within a geographic location must include animal sources other than swine, although such nonporcine species usually are dead-end hosts. Domestic livestock (cattle, goats, sheep) 3,5,13,14,25,30,35 and wildlife (wild rats, mice, mink, fox, deer, badger, coyotes, hare, raccoons) 21,28,37 are susceptible to natural ADV infections. Deaths from ADV infections also may occur in cats and dogs residing on or near premises with infected livestock. 4,6,15,16,20,22,23,31 Moreoever, ADV was genetically stable during in vivo passage through nonporcine species. 33 Epidemiologic applications of REA include documenting the occurrence of new ADV strains in an area and classifying isolates from a geographic location into groups to infer viral transmission. In this regard, REA was performed on ADV isolated from moribund lambs. 38 The infected lambs had both fence line contact with swine and exposure to a syringe, which had previously been used to vaccinate swine with a modified live ADV product. The resultant patterns indicate...