Summary: We describe an integrated java-based program that provides elaborate graphic and plain-text output of pairwise linkage disequilibrium (LD) analysis of single nucleotide polymorphisms genotypic data. It is most suitable for molecular geneticists, who are focusing on LD measures estimation, statistical significance test and extent prediction. Availability: The software is available at: http://www.chgb.org.cn/lda/lda.htm Supplementary information: Detailed tutorials, LDA help system and examples are distributed within LDA software. For Macintosh OS X user, the Jre version 1.4 can be downloaded from http://connect.apple.com