The Alternaria and Ulocladium species reported from humans are studied taxonomically using rDNA internal transcribed spacer (ITS) sequence data. The ITS variability within the genus is relatively limited. The two most important, longicatenate species, Alternaria alternata and A. infectoria, clearly differ in their ITS domains, due to a 26-bp insert in ITS1 of the latter species. A number of taxa inhabiting particular plant species, such as A. longipes on tobacco and A. mali on apple, but also the common saprobic species A. tenuissima cannot reliably be distinguished from A. alternata using this method. The large number of described noncatenate, obligatory plant pathogens are extremely rare as agents of human disease; clinical routine identification does not need to include these taxa. The predictivity of a simplified polymerase chain reaction-restriction fragment length polymorphism procedure of rDNA for the recognition of the relevant species or species aggregates is established in a randomized test. The method was found to be rapid and cost-effective. Its efficacy extended to the identification of sterile and meristematic Alternaria strains, some of them previously classified in genera such as Chmelia and Botryomyces. Microscopic morphology and some additional tests remain necessary to allow identification of the aggregates of potential etiological agents of human disease. About 14% of the sequences deposited in GenBank were found to be misidentified. Alternaria infectoria is one of the most common clinical Alternaria species, despite its low degree of melanization. The lack of pigmentation has frequently led to misidentification of such isolates.