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The purpose of this study was to evaluate clinical cases of cat scratch disease (CSD) and bacillary angiomatosis involving the conjunctiva by special stains and transmission electron microscopy (TEM) and to compare these findings with the results from species-specific polymerase chain reaction (PCR) analysis of the same specimens.Six potential cases of CSD and 2 possible cases of bacillary angiomatosis of the conjunctiva were analyzed by light microscopy, the Warthin-Starry technique, TEM, and PCR. DNA isolated from cultured Bartonella henselae, B. bacilliformis, B. quintana, and B. elizabethae were used as control templates for establishment of the PCR sensitivity and specificity. Cultured DNA was also used as appropriate positive controls during analysis of the clinical specimens.The histological studies, electron microscopy, and the PCR analysis confirmed the identification of the bacilli within the involved tissues. Furthermore, molecular diagnosis by PCR allowed for speciation of the infecting Bartonella organisms in 6 of the 8 cases and correlated with the histological findings.The PCR-based identification of Bartonella correlated well with the results of light microscopy and TEM and provided a simple and rapid method of diagnosis to the species level. The molecular analysis may prove to be beneficial in enhancing the current diagnostic techniques for CSD and bacillary angiomatosis.