The aminoalcoholphosphotransferase is the key gene in the biosynthesis of phosphatidylcholine in Arabidopsis. Evaluating the effect of the second isoform of that gene, a T-DNA insertion mutant i. e. aapt2 was used. Comparison of aapt2 and wild type (WT) showed this line differs in the number of traits. There was a very significant difference between aapt2 and WT regarding the days that plant reach to two, three, four, five and six rosette leaves, final rosette size, 10% of flowers to be produced and flowering complete. For the days that plant reach to 8, 9, 10, 11, 12 and 13 rosette leaves, first flower buds visible, first flower open, 30% and 50% of flowers to be produced and the first silique shattered; the significant difference between aapt2 and WT has been observed. There was no difference for the days that plant reach to 14 rosette leaves, rosette is 20, 50 and 70% of final size and senescence complete between aapt2 and WT. These likely suggested that the protein encoded by the AAPT2 plays a role in the early stages of Arabidopsis growth. Also, aapt2 and WT were very significantly different in osmotic pressure, but the relative content of water, chlorophyll a and b, carotenoids, peroxidation of membrane lipids, stomatal resistance and photochemical efficiency of photosystem II did not show any significant differences. Also, the aapt2 and WT were significantly different for leaf number and fresh and dry weight of leaves, however; the fresh and dry weight of root was not different.