Little is known about how the sweet potato (Ipomoea batatas) root system responds to Ceratocystis fimbriata in the growth substrate. Understanding whether the fungus affects the root system before harvest of storage roots (SR) could guide timing of management efforts. Cuttings of cultivars Bayou Belle and Beauregard, both previously considered susceptible to black rot, were in unamended or infested sand. At the onset of SR formation, effects on first‐ and second‐order lateral root (LR) length and number among and within treatments, cultivars and replicate experiments were recorded. First‐order LR length in inoculated Bayou Belle plants was 31% greater than in inoculated plants of cultivar Beauregard in Expt 1, but there were no differences in Expt 2. Second‐order LR length varied among, and within, cultivars, inoculum treatments and experiments in Expts 1 and 2. At 49 days after planting in Expt 1, only inoculated plants had necrotic lesions on stems in both cultivars, with more than twice as many recorded on Bayou Belle than Beauregard. SR had no lesions at harvest. Detached SR originating from inoculated treatments and stored in sampling bags for 25 days developed black rot lesions at either end of the SR (45% and 31% of total in Expt 1 and Expt 2, respectively) or elsewhere, including those centred on LR emergence sites or lenticels (55% and 69%, respectively). Exposing developing plants to inoculation may reveal differences in SR susceptibility not found when harvested SR are wounded and inoculated. [ABSTRACT FROM AUTHOR]