We propose the use of multivariate analysis of variance in order to address linkage relationships between a genetic marker and a phenotype that is specified by multiple variables. Moreover, enhanced power of a linkage model that simultaneously accounts for environmental factors is demonstrated in the present study. This strategy was used to establish linkage of a quantitative trait locus influencing ethanol-induced anesthesia to the albinism gene (Tyr) in mouse. This approach, which can be implemented immediately with most statistical packages, provides the extreme flexibility of multivariate analysis of variance for analyzing complex questions of linkage regarding either animal or human research paradigms.