Humans and other animals with Lyme borreliosis produce antibodies to a number of components of the agent Borrelia burgdorferi, but a full accounting of the immunogens during natural infections has not been achieved. Employing a protein array produced in vitro from 1,292 DNA fragments representing ϳ80% of the genome, we compared the antibody reactivities of sera from patients with early or later Lyme borreliosis to the antibody reactivities of sera from controls. Overall, ϳ15% of the open reading frame (ORF) products ( Infectious disease research has advanced rapidly with the accumulation of whole-genome sequences of pathogens and the subsequent use of genome-wide DNA microarrays to study gene expression. Equipped with arrays in different formats, investigators have identified different genes in a variety of pathogens that are more highly expressed in host animals or under in vitro conditions mimicking the in vivo environment. With few exceptions (27), these array studies have been performed with experimental animals, usually rodents, and in laboratory settings. Less is known about the proteins that are expressed during natural infections of humans or other host animals. Detection of a specific antibody during the course of infection is indirect evidence of in vivo expression by the pathogen. But the use of this approach to study large numbers of proteins has been largely limited to one-dimensional and two-dimensional gel electrophoresis of whole cells having an in vitro origin, followed by identification of the more abundant antigens by partial amino acid sequencing of reactive bands or spots and then searches of the databases (22,23,38,44,52,60,66).An alternative to using the pathogen itself as the source of the proteins is to produce recombinant polypeptides based on the deduced open reading frames (ORFs) of the pathogen's genome and to determine whether these polypeptides are antibody targets (11,61). A potential shortcoming of using this approach with cells, such as Escherichia coli or yeast (Saccharomyces cerevisiae) cells, is that some foreign proteins may not be expressed or the quantity may be insufficient. Felgner and coinvestigators increased the success rate for expression and decreased the cost with a high-throughput, cell-free, coupled transcription-translation system (26,29,30). Hundreds to thousands of individual recombinant proteins are printed on chips, which are then used to capture antibodies present in serum from infected individuals and other animals. The amount of captured antibody is quantified using a labeled secondary antibody. Whole-proteome microarrays have been employed in studies of experimental Francisella tularensis infections in laboratory mice (35,57) and of immune responses of humans to immunization with live vaccinia virus (26,29,31). McKevitt et al. (61) and Brinkmann et al. (11) used the enzyme-linked immunosorbent assay (ELISA) format to study the binding of antibodies of experimentally infected rabbits and people with syphilis to a nearly complete representation of the OR...