A nonparametric method for linkage analysis has been developed and applied to the Problem 1 data set of the Genetic Analysis Workshop 9. Basically, the univariate matched pair strategy of the transmission disequilibrium test has been adapted to multivariate modeling using the conditional logistic function. After setting the critical value for significance at p ⩽ 0.0001, models at only D5G23 and D1G31 appear to be significant (p < 10−7). Logistic transmission modeling is a powerful method for establishing linkage by disequilibrium. ©1995 Wiley-Liss, Inc.