B. bacilliformis is a small, gram-negative, motile organism with a brush of ten or more unipolar flagella. It is an obligate aerobe that grows best at 28°C in semisolid nutrient agar with 10% rabbit serum and 0.5% rabbit hemoglobin.

The vector of this disease is the sand fly, Phlebotomus noguchi. After inoculation, Bartonella enter the endothelial cells of the blood vessels, where they proliferate during the incubation period. These organisms, which can be found throughout the reticuloendothelial system and in many specific organs, then reenter the bloodstream and parasitize the erythrocytes. The resulting hemolytic anemia is caused by the destruction of these parasitized cells, which may constitute as many as 90% of the erythrocytes. Patients who survive the acute phase of Oroya fever may or may not develop the cutaneous manifestations of the disease, which appear as nodular hemangiomatous lesions or verrucae ranging in size from a few millimeters to several centimeters.

The incubation period ranges from 2 to 14 weeks. In patients who are totally asymptomatic, diagnosis can be obtained only by blood culture. Other patients may develop such symptoms as headache, malaise, and occasional fever without anemia despite recovery of B. bacilliformis from blood cultures. Patients with severe anemia or Oroya fever are febrile, and Bartonella can be observed parasitizing the erythrocytes. The anemia develops rapidly, and patients present with a peculiar discoloration of the skin and sclera caused by the combination of slight icterus and severe anemia. Often, other symptoms referable to severe anemia are present. Delirium and clouding of the sensorium are rather common symptoms that usually are mild but may progress to overt psychosis. On physical examination, the signs of severe anemia and icterus may be accompanied by generalized lymphadenopathy.