The occurrence of sudden infant death syndrome (SIDS) has been linked to several genetic risk factors, e.g. genes involved in the neuroadrenergic system, variations in serotonin reporter genes or mutations in long-QT syndrome genes. Additionally, polymorphisms in genes with impact in sleep disorder syndromes have been proposed to be of importance as genetic risk factors for SIDS. In this study, we investigated the polyalanine length variation of PHOX2B and the -794 CATT repeat in the MIF promoter region as well as single nucleotide polymorphisms (rs28462174, rs28727473, rs16853571, rs755622, rs12485058, rs12485068, rs4822444, rs4822445, rs4822446, rs4822447 and rs2012124) in both genes in 278 SIDS cases and 240 controls. No significant differences were found in allele distribution of neither length polymorphisms nor single nucleotide polymorphisms between SIDS cases or controls. Therefore, an importance of these variations for the occurrence of SIDS could be ruled out.