Calcium ion (Ca²⁺) signaling is a typical phenomenon mediated through immune receptors, such as the B-cell antigen receptor (BCR) and it is important for their biological activities. To analyze the signaling of immune receptors together with their in vivo dynamics, we generated stable transgenic mice with the Föster/fluorescence resonance energy transfer (FRET)-based Ca²⁺ indicator yellow cameleon 3.60 (YC3.60), based on the Cre/loxP system (YC3.60^flox). We successfully obtained mice with specific YC3.60 expression in immune or nerve cells as well as mice with ubiquitous expression of this indicator. We established five-dimensional (5D) (x, y, z, time and Ca²⁺) intravital imaging of lymphoid tissues, including the bone marrow. Furthermore, in autoimmune-prone models, the CD22^−/− and C57BL/6- lymphoproliferation (lpr)/lpr mouse, Ca²⁺ fluxes were augmented, although they did not induce autoimmune disease. Intravital imaging of Ca²⁺ signals in lymphocytes may improve assessment of the risk of autoimmune diseases in model animals.