HaploPainter is a user-friendly pedigree-drawing application with special features for easy visualization of complex haplotype information. It has been developed to facilitate gene mapping in Mendelian diseases in terms of fast and reliable definition of the smallest critical interval harbouring the underlying gene defect. HaploPainter is written in Perl and may be used for visualization of haplotypes calculated by any of the common linkage programs. With special features like haplotype compression or the ability of marker section cut-out it particularly addresses the requirements for viewing large haplotypes as obtained by using for genome scans high-density marker panels of many thousands of single nucleotide polymorphisms (SNPs).