As the world’s population ages, the incidence of chronic lymphocytic leukemia (CLL) will continue to increase. CLL-related autoimmune cytopenias (AICs) are becoming a growing challenge in daily clinical practice. AICs occur in c.10% of CLL patients, and include autoimmune hemolytic anemia, immune thrombocytopenia, pure red cell aplasia, and autoimmune granulocytopenia. The complication can appear at any disease stage, both in treated and previously untreated patients. In some cases, AICs precede the diagnosis of the underlying disease. The diagnostic process of autoimmune complications is often difficult. First of all, however, it requires differentiation from bone marrow infiltration resulting from underlying disease progression. A properly established diagnosis has prognostic and therapeutic implications. Autoimmune cytopenias are more often associated with high-risk CLL (with 17p deletion, 11q deletion, wild-type variant of gene encoding immunoglobulin heavy chain variable region) and show a complex pathogenesis. CLL cells and the surrounding microenvironment are involved in autoimmune mechanisms. Treatment of AICs depends on CLL stage. In the case of isolated symptoms of AICs, without accompanying features of CLL progression, glucocorticosteroids or rituximab are recommended in the first line treatment. No response or a suboptimal response to treatment implies further therapeutic decisions. According to significant advances in the treatment of chronic lymphocytic leukemia, therapeutic strategies for autoimmune cytopenias also need to be optimized. The widespread introduction of ibrutinib, idelalisib, and venetoclax has highlighted the need for understanding the interplay between targeted therapies and AICs.