The International Potato Center (CIP), near Lima, Peru, holds one of the largest clonal collections of tetraploid (2n = 4x = 48) Andean farmer selected potato cultivars (Solanum tuberosum L. subsp. andigena Hawkes). CIP selected a core collection of 306 Andean cultivars from the 2379 accessions available in the genebank to facilitate the utilization of these genetic resources. Our objective was to investigate the genetic structure in both the entire collection and its respective core subset with nine isozyme markers that have been genetically characterized. Such an analysis provides a means to validate the sampling strategy of the core collection. Allozyme frequencies and average heterozygosity were calculated for each locus investigated. The allozyme frequency distribution for each locus was tested for homogeneity between the entire and core collections by X2 tests. A total of 38 allozymes were scored in the entire collection. Only two rare allozymes (Idh-13 and Pgi-15) with a gene frequency (q) of 0.0002 (or 0.02%) were not included in the core collection. The most frequent allozymes in the entire collection also showed the highest frequencies in the core collection. The allozyme frequency distributions were also homogeneous (P > 0.05) for all loci except for the Pgi-1 and Got-1 loci. Average locus heterozygosity was similar (P > 0.05) between the entire and core collection (49 and 50%, respectively). This analysis suggests that the sampling strategy to develop this core collection of tetraploid Andean potato cultivars was adequate to capture a representative sample of the allozyme loci, because only rare alleles (q < 0.0005 or 0.05%) were lost in the selected core subset. Therefore, this core collection may be an appropriate entry point for researchers who wish to utilize the genetic diversity of this gene pool more efficiently.