Aim: The aim in this survey was to study the clinical characteristics of infections caused by Borrelia genospecies in patients with erythema migrans where Borrelial origin was confirmed by polymerase chain reaction. The aim was also to study factors influencing the clinical appearance of erythema migrans. Methods: The study was conducted in southern Sweden from May 2001 to December 2003 on patients 18 years and older attending with erythema migrans at outpatient clinics. All erythema migrans were verified by polymerase chain reaction, photographed and categorized into “annular” or “non-annular” lesions. A logistic regression model was used to analyze relations between the appearance of the erythema migrans (i.e., annular or non-annular) and factors that influenced its clinical appearances. Results: A total of 118 patients, 54 women (45.8%) and 64 men (54.2%), fulfilled the inclusion criteria. Of these patients, 74% were infected by B. afzelii, 26% by B. garinii ( p < 0.001). A total of 45% (38/85) of the erythema migrans were annular, 46% (39/85) were non-annular and 9.4% (8/85) were atypical. For men infected by B. afzelii the odds ratio of developing non-annular erythema migrans was 0.09 (95% CI: 0.03 - 0.33) in comparison with women with the same infection. Conclusions: In this prospective study of a large series of erythema migrans, where infecting genospecies were confirmed by polymerase chain reaction, the sex of patients infected with B. afzelii had a strong influence on the appearance of the rash. Patients infected by B. garinii more often had non-annular erythema migrans and a more virulent infection with more individuals presenting with fever, raised levels of C-reactive protein and seroreactivity in the convalescence sera.