We report a human case of leptospirosis in which the spirochete was detected by dark-field microscopy examination of cerebrospinal fluid (CSF) and isolated from both CSF and blood. Leptospira fainei was identified by sequencing the 16S rDNA gene, which had been amplified by polymerase chain reaction. This case confirms the role of L. fainei as a human pathogen and extends its distribution to southern Europe.