Huanglongbing (HLB) is a devastating disease of citrus and threatens the citrus industry worldwide. The suspected causal agent of the disease is a phloem-limited bacterium of the genus Candidatus Liberibacter transmitted through insect vector or grafting with diseased budwood. Currently, most seed source trees for citrus rootstock propagation are located outdoors and unprotected from disease transmission. In addition, fruit from HLB-affected scion varieties in Florida containing seeds enter the commercial trade and move into other citrus-growing areas. The objective of this study was to determine how Ca. L. asiaticus infection affects seed quality and seedling development and whether the disease appears in seedlings grown from infected fruit. Two experiments were conducted involving thousands of seedlings produced from seeds from infected rootstock seed source trees and ‘Valencia’ sweet orange trees, respectively. Infection of trees and fruit with Ca. L. asiaticus significantly reduced seed weight, seed germination, and seedling height. Seedlings did not develop symptoms typical of HLB throughout the experiment. Polymerase chain reaction (PCR) analysis initially identified two of 686 rootstock seedlings and three of 431 sweet orange seedlings positive for the pathogen when they were very young. Resampling and PCR analysis of these five seedlings at older ages consistently indicated they were negative for the pathogen and none of these plants ever developed symptoms of HLB. It is suggested that Ca. L. asiaticus may have been translocated into some part of the embryo during seed development but that it was not present in cells or tissue, which permitted replication or disease development as the seedling grew.