To assess physician preferences in the diagnosis and treatment of Lyme disease, questionnaires were sent to physicians in various Lyme disease endemic areas in the U.S. Seventy-eight responses were analyzed. Both ELISA and Western blot were ordered by 86% of responders. Fifty percent of responders believed that 25% or more of patients who have Lyme disease were seronegative. The treatment was influenced by physician specialty. Antibiotic treatment for tick bite was prescribed by 20% of responders. Erythema migrans rash was treated by all responders without serologic confirmation. The median treatment duration of erythema migrans was 4 weeks. For post-erythema migrans Lyme disease, 43% of responders treat 3 months or more; for chronic Lyme disease, 57% of responders treat 3 months or more. Our survey documents significant differences between published recommendations and actual practices. Physician education and clinical trials are needed to clarify the reasons for these differences.