Abstract Motivation: Genetic linkage analysis is a useful statistical tool for mapping disease genes and for associating functionality of genes with their location on the chromosome. There is a need for a program that computes multipoint likelihood on general pedigrees with many markers that also deals with two-locus disease models. Results: In this paper we present algorithms for performing exact multipoint likelihood calculations on general pedigrees with a large number of highly polymorphic markers, taking into account a variety of disease models. We have implemented these algorithms in a new computer program called superlink which outperforms leading linkage software with regards to functionality, speed, memory requirements and extensibility. Availability: superlink is available at http://bioinfo.cs.technion.ac.il/superlink Contact: fmaayan@cs.technion.ac.ildang@cs.technion.ac.il Keywords: Bayesian networks; Fastlink; Genehunter; linkage analysis; Vitesse.