Atopy and autoimmunity are usually considered opposed immunological manifestations. Lyn -/- mice develop lupus-like autoimmune disease yet have coexistent intrinsic allergic traits and are prone to severe, persistent asthma induced exogenously. Recently it has been proposed that the Th2 environment and IgE auto-Abs promotes autoimmune disease in Lyn -/- mice. To examine this apparent contradiction, we derived Lyn -/- mice with a null mutation in STAT6, a regulator of Th2 immunity that integrates signaling from the IL-4/IL-13 receptor complex. Atopy and spontaneous peritoneal eosinophilia, characteristic of Lyn -/- mice, were lost in young Lyn -/-STAT6 -/- mice; however, autoimmune disease was markedly exacerbated. At a time-point where Lyn -/- mice showed only mild autoimmune disease, Lyn -/-STAT6 -/- mice had maximal titres of IgG and IgA auto-Abs, impaired renal function, myeloid expansion and a highly activated T cell compartment. Remarkably, low level IgE auto-Abs but not IgG1 auto-Abs were a feature of some aged Lyn -/-STAT6 -/- mice. Furthermore, aged Lyn -/-STAT6 -/- mice showed dramatically increased levels of serum IgE but minimal IgG1, suggesting that class-switching to IgE can occur in the absence of an IgG1 intermediate. The results show that Lyn-deficient mice can overcome the effects of disabling Th2 immunity, highlighting the importance of Lyn in controlling Th2 responses. Our data also indicates that, under certain conditions, STAT6-independent factors can promote IgE class-switching. This work has important clinical implications as many experimental therapies designed for the treatment of asthma or atopy are based on targeting the STAT6 axis, which could potentially reveal life endangering autoimmunity or promote atopy in susceptible individuals. A? 2012 Elsevier Ltd. All rights reserved.