Biological markers or endophenotypes may be used to help delineate the relationships between underlying trait genotypes and trait phenotypes. However, analyzing quantitative biological markers jointly with a qualitative trait phenotype (affected versus unaffected) for linkage with genetic marker loci is not straightforward. For the situation in which both the biological marker(s) and the qualitative trait phenotype are under the control of underlying genotypes, a simple method is developed for jointly using biological marker and trait phenotype in linkage analysis. An example demonstrates its implementation in the LINKAGE programs.