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Because they deal with many distinct but rare inheritance diseases, geneticists have difficulty translating from their codes to other biomedical coding schemes. The objective of this research was to investigate the potential uses and difficulties of using the UMLS Metathesaurus for genetic diagnoses and to make recommendations to UMLS developers for improvements in UMLS for common genetic disorders. The 110 most common Mendelian Inheritance in Man disorders from the Missouri Genetic Disease Program over the period of one year were translated into MeSH, ICD and SNOMED. The more common diseases are more likely to be mapped than the rarer ones. Diseases with a proven genetic inheritance pattern are more likely to be mapped than those with speculated inheritance patterns. Approximately one third of all diagnoses were not mapped across all three coding schemes in Meta-1.2. The ICD coding scheme was found to be too broad to be meaningful for genetic diagnosis or epidemiological purposes. MeSH and SNOMED need to be made more specific and complete, and all of the new version of SNOMED needs to be included in the Metathesaurus.