Background/Aims: Lipoatrophy (LA) is a rare, possibly under-recognised side effect of insulin treatment of unclear aetiology. The aim of this study was to describe the characteristics of patients with type 1 diabetes (T1D) who have LA and to explore the relationship between LA and other autoimmune diseases based on the hypothesis that additional autoimmune phenomena are more prevalent in T1D patients with LA. Methods: This was a cross-sectional observational study of T1D patients with LA in comparison to T1D patients without LA who are registered with the Diabetes Patienten-Verlaufsdokumentationssystem database of 241,650 patients in Germany and Austria. Results: Hashimoto's thyroiditis and coeliac disease were more prevalent in patients with LA (p < 0.001 for both). LA was associated with an increased risk of Hashimoto's thyroiditis and coeliac disease in female patients [odds ratio (OR) 2.5, p = 0.003, and OR 3.1, p = 0.02, respectively]. This relationship persisted after adjustment for current age, duration of diabetes and calendar year of treatment (OR 2.7, p = 0.002, and OR 3.5, p = 0.01, respectively). Conclusion: These findings support the hypothesis that an immune complex-mediated inflammatory process may be important in the development of LA.