While recent genomic surveys reveal growing numbers of di-allelic copy number variations, it is genes with multiallelic (>2) copy numbers that have shown association with distinct phenotypes. Current high-throughput laboratory methods are restricted to enumerating total gene copy numbers (GCNs) per individual and not the "genotype," i.e. gene copy per chromosome. Thus, association studies of multiallelic GCNs have been limited to comparison of median copies in different groups. Our new nonparametric statistical approach is based on GCN information within a trio-based study design. We present theoretical derivation of the statistics and results of simulation studies that show robustness of our approach and power under several genetic models. © 2009 Wiley-Liss, Inc.