Inhibition of "Calypso" cucumber seedling growth by rye allelochemicals, 2(3H)-benzoxazolinone BOA and 2,4-dihydroxy-1,4(2H)-benzoxazin-3-one DIBOA, was studied by analyzing the growth of seedling tissues and organs. Light and electron microscopy of seedling root cells were also carried out to investigate the mechanism(s) of root growth inhibition and mode of action of these compounds. BOA inhibited root elongation and reduced the number of cucumber lateral roots by 77 and 100% at 0.1 and 0.43 mg BOA/ml deionized (DI) water, respectively. DIBOA also inhibited root growth, but did not affect the number of lateral roots. BOA increased size of cucumber cortical root cells fivefold, but DIBOA had no effect. Both compounds reduced the regeneration of root cap cells and increased the width of cortical cells resulting in increased root diameter. BOA and DIBOA caused increased cytoplasmic vacuolation, reduced ribosome density and dictyosomes, reduced number of mitochondria, and reduced lipid catabolism. Starch granules in amyloplasts of seedling roots treated with BOA and DIBOA were also greatly reduced compared to the control. Changes in cellular ultrastructure indicated that BOA and DIBOA reduced root growth by disrupting lipid metabolism, reducing protein synthesis, and reducing transport or secretory capabilities.