Based on a survey of academic training programs and an analysis of advertised job openings, we conclude that the labor market in bioinformatics has changed dramatically from the 1990s to the early 2000s. The number of academic training programs, as well as enrollment in these programs, expanded rapidly during this period. The expansion has created a sizeable pipeline of students who will matriculate from these programs in the near future. Yet, at the same time that this expansion in training programs occurred, demand in the bioinformatics market declined and its origins have shifted largely from industry to academe. Unless conditions in industry change dramatically in the next few years, it is likely that trainees from these programs will have difficulty finding the expected jobs in industry.