Histocompatibility typing allows the matching of patients and donors in organ transplantation, and the accuracy of HLA matching influences to a great extent the clinical outcome. Recent breakthroughs in the molecular biology of HLA class II genes have revealed that the degree of HLA diversity and polymorphism is in fact much greater than was expected on the basis of the traditional serological HLA typing assays. In parallel, it has become possible to analyse this extensive polymorphism directly at the level of the HLA class II genes and of their DNA sequences. We have described a DNA typing procedure referred to as 'HLA oligotyping' which is based on the hybridisation of allele and loci specific oligonucleotide probes. This procedure has now become operational on a large scale and this review describes the principles and major applications of the technique. It consists in the hybridisation of DNA with informative sequence-specific oligonucleotide probes, following an amplification of DNA in vitro by the polymerase chain reaction (PCR). The use of this highly sensitive technique for HLA-DR, -DQ and -DP typing is discussed, focusing on the clinical applications in the field of organ transplantation, particularly for bone marrow transplantation with unrelated donors. It now allows the unambiguous identification of all HLA subtypes, including those that cannot be recognised otherwise, and it represents powerful complement to current methods of HLA typing. Finally this methodology is widely used in HLA-disease association studies, aiming at the characterisation of HLA class II epitopes involved in the susceptibility or resistance to autoimmune diseases.