Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis. We identified 506 PAMP-induced differentially alternatively spliced (DAS) genes. Although many DAS genes are targets of nonsense-mediated degradation (NMD), only 19% are potential NMD targets. Importantly, of the 506 PAMP-induced DAS genes, only 89 overlap with the set of 1849 PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DAS events. Global DAS analysis of mpk3, mpk4, and mpk6 mutants revealed that MPK4 is a key regulator of PAMP-induced differential splicing, regulating AS of a number of splicing factors and immunity-related protein kinases, such as the calcium-dependent protein kinase CPK28, the cysteine-rich receptor like kinases CRK13 and CRK29 or the FLS2 co-receptor SERK4/BKK1.These data suggest that MAP kinase regulation of splicing factors is a key mechanism in PAMP-induced AS regulation of PTI.