An association between borreliosis and autoimmune thyroid disease (AITD) has previously been discussed. We undertook the present analyses to explore associations between anti-Borrelia immunoglobulin G (IgG) and AITD using data from the population-based Study of Health in Pomerania (SHIP), which was conducted in a region with endemic Borreliosis. Data of 4,256 persons were available for the present analyses. IgG antibodies to Borrelia were determined by enzyme-linked immunosorbent assay (ELISA). AITD was defined as the combined presence of a hypoechogenic thyroid pattern in thyroid ultrasound and positive anti-thyroperoxidase levels. An association between anti-Borrelia IgG and AITD was neither present in bivariate nor in multivariate statistical analyses. This result was not affected by using different definitions of the exposure and the end points. There is no association between the exposure to Borrelia as defined by anti-Borrelia IgG and the risk of AITD. It seems unlikely that Borrelia species represent a relevant causal factor for AITD.