SUMMARY Agrobacterium‐mediated transformation enables random transfer‐DNA (T‐DNA) insertion into plant genomes. T‐DNA insertion into a gene's exons, introns or untranscribed regions close to the start or stop codon can disrupt gene function. Such T‐DNA mutants have been useful for reverse genetics analysis, especially in Arabidopsis thaliana . As T‐DNAs are inserted into genomic DNA, they are generally believed to be stably inherited. Here, we report a phenomenon of reversion of intronic T‐DNA mutant phenotypes. From a suppressor screen using intronic T‐DNA pi4kβ1,2 double mutant, we recovered intragenic mutants of pi4kβ1 , which suppressed the autoimmunity of the double mutant. These mutants carried deletions in the intronic T‐DNAs, resulting in elevated transcription of normal PI4Kβ1 . Such reversion of T‐DNA insertional mutant phenotype stresses the need for caution when using intronic T‐DNA mutants and reiterates the importance of using irreversible null mutant alleles in genetic analyses.