Alternate bearing is a significant economic problem adversely affecting the producers, consumers, and economy of a country. In the present study, we aimed to investigate the physiological role of free polyamines (PAs) in fruit bud abscission of the Uzun pistachio variety, which has a strong alternate bearing tendency. The identification and quantification of PAs, such as putrescine (Put), spermidine (Spd), and spermine (Spm), at different physiological stages and in different organs, were carried out by high-performance liquid chromatography. Putrescine was the major PA in all the organs of pistachio trees. Furthermore, the concentrations of Put and Spd in the leaves and shoots sharply declined and reached the minimal levels during the fruit bud abscission period (June), and then increased during the period of kernel development. The concentration of Put and Spd in the panicles increased gradually until the beginning of kernel growth and then decreased until harvest. The concentration of Spm exhibited a negative correlation between shoots and leaves, especially in the 'On-year' trees. There was a significant decrease in PAs in the leaves during the period of bud abscission in the 'Off-year' trees. In the 'On-year' trees, the concentration of PAs exhibited a negative correlation with the panicles, especially when the concentration of Put and Spd increased during the kernel development period, and then decreased. The concentration of PAs in the panicles of the 'On-year' trees was higher than that in the nuts, and it exhibited a negative correlation with that in the nuts. The results suggest that PAs might lead to physiological changes during the growth and development stages of pistachios, and a strong relationship was observed.