Transport of nucleic acids through cell membranes is an essential biological process that occurs in all living organisms. This review focuses on two plant systems in which nucleic acid molecules are transported through membrane channels: transport of Agrobacterium T-DNA through nuclear pores and movement of plant viruses through intracellular connections. To provide a broader perspective, nuclear uptake of animal viruses and nuclear import/export of small nuclear (sn) RNA and messenger (m) RNA are described. By comparing the examined cases of nucleic acid transport, the review proposes a set of general rules for this type of transport through membrane channels.