Regulated cell death is an essential piece of normal development and maintenance of tissue homeostasis, wherein BCL2 like 1 (BCL2L1) protein is involved in key signaling pathways. Alternative splicing in exon 2 of Bcl2l1 produces Bcl-x short (Bcl-xS) isoform. However, mutations in around 5’ splice site are classified as variants of uncertain significance in humans, and the isoform-specific role of endogenous Bcl-xS remains largely unexplored. Here we show the role of Bcl-xS in vivo by generating the mice with a mutation in 5’ splice site of the Bcl2l1 that inhibits Bcl-xS alternative splicing. Although loss of BCL2L1 leads to embryonic lethal with massive cell death, Bcl-xS knockout (KO) mice were born at a mendelian ratio and showed no overt abnormality until 3 months of age. Thereafter, the KO mice developed cardiac hypertrophy (heart weight/tibia length, 8.59+/-0.308 vs 11.61+/-0.631, p = 0.0005 and 2.13-fold increase in individual cardiomyocyte size, p = 0.0001) with contractile dysfunction (EF, 69.25+/-1.31 vs 56.57+/-3.07, p = 0.0028) and splenomegaly (spleen weight/tibia length, 5.32+/-0.25 vs 7.12+/-0.49, p = 0.0051) at 6 months of age. Despite that overexpression of Bcl-xS induced cell death in cardiomyocytes (2.497-fold compared to LacZ, p < 0.0001), there was unexpectedly no overt difference in the level of apoptosis in the KO heart (TUNEL, 0.033+/-0.003 vs 0.030+/-0.002 %, p = 0.359), but fibrosis was significantly increased in the KO heart (1.602+/-0.095 vs 2.340+/-0.145 %, p = 0.0017). Diabetes was not evident in the KO mice (blood glucose, 169.8+/-10.9 vs 153.3+/-8.46 mg/dl, p = 0.2595). Mechanistically, we found that the Akt/mTOR and JNK/cJun signaling are activated in the KO heart and the JNK/cJun signaling is activated with increased Bax expression in the KO spleen. These results suggest that Bcl-xS may be dispensable for development, but is essential for maintaining homeostasis of multiple organs, especially cardiosplenic network, in a tissue-dependent mechanism.