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Current trends in the bioinformatics job market were assessed using a sample of 1,996 online employment advertisements from the 6-year period of January 2003 through December 2008. Job postings were classified by employer type, job role, and location, and a content analysis of the text of a subset of 404 of the posts was performed to identify detailed characteristics associated with master's degree level positions, such as educational requirements and preferred scientific and technical skills. Consistent with previous studies, academic institutions, corporations, and research institutes are the primary employers of bioinformaticists. In the U.S. only three states, California, Maryland, and Massachusetts, provided the majority of opportunities. Graduates from all levels of education are needed in the field, although those with a bachelor's degree in computer science or a Ph.D. in biology or bioinformatics are especially in demand. Perl programming is the most frequently requested skill across advertised positions, and experience using bioinformatics software tools (such as BLAST, CLUSTAL, and HMMER) is the bioinformatics skill in greatest demand. A small number of positions specifically requesting librarians and LIS-trained bioinformaticists was observed, but the significant bioinformatics activities in biomedical libraries over the same time period are not reflected in this snapshot of the bioinformatics workforce.