Shoot tips of potted Empire and Golden Delicious trees on the susceptible dwarfing rootstock M.26 in the greenhouse were injected with inoculum containing 5 × 109 CFU/ml Erwinia amylovora. At intervals after inoculation, trees were sampled at increments between the shoot tip and the roots by excising stem segments. Segments were ground in phosphate buffer and assayed for the presence of E. amylovora by plating on semi-selective medium and by a polymerase chain reaction (PCR)-based detection method. Eleven days after inoculation, E. amylovora was detected by PCR in symptomless scion tissue >50 cm below the shoot-tip in Empire and Golden Delicious, and in 2-year-old tissue in Golden Delicious. By 21 days, E. amylovora was detected in the M.26 rootstock of Empire trees, and by 41 days in the M.26 rootstock of Golden Delicious. In a similar experiment the following year, Empire trees on M.26 rootstock were inoculated with E. amylovora at early (16 May), mid- (11 June), and late (6 July) phenophase of shoots. Three weeks after inoculation, E. amylovora was detected by PCR from M.26 rootstocks of five of six plants inoculated at the late phenophase, compared to zero of six plants inoculated at the early or mid-phenophase. Late-season fire blight infections of the scion may be particularly hazardous for the health of the rootstock.