In tissue culture of Lilium, the standard initiation procedure brought about substantial contamination in two ways. (1) When scales were detached from the mother bulb, microorganisms could enter via the wound. This source of contamination was strongly enhanced by the negative hydrostatic pressure within the scales by which nonsterile fluid was sucked up at detachment. Contamination decreased strongly when the scales were detached from bulbs submerged in 0.03% NaClO. Evidence is presented that this type of contamination was endogenous, i.e., localized in the interior of the explant. (2) During the rinsing of scales after surface-sterilization, the rinsing water became contaminated with microorganisms associated with the scales that had not been killed during surface-sterilization. This caused cross-contamination. This type of additional contamination was controlled by rinsing in 0.03% NaClO instead of ‘sterile’ water. In our conditions, these initiation-related sources of contamination led to ca. 20% and ca. 25% contamination, respectively, of otherwise uninfected scales.