For tissue engineering applications, small interfering RNA (siRNA) is an attractive agent for controlling cellular functions and differentiation. Although polyionic condensation of nucleic acids with polycations has been widely used for gene delivery, siRNA is not strongly associated with cationic carriers due to its low charge density and rigid molecular structures. The use of an excess amount of cationic carriers is often used for siRNA condensation, though they can induce severe cytotoxicity. Here we introduce the self-assembly of siRNA with mild polyelectrolytes into multilayers for efficient gene silencing during cell proliferation. The multilayers were prepared through the sequential layer-by-layer deposition of siRNA and poly-L-lysine (PLL) on a polydopamine-coated substrate. The cells, grown on the siRNA/PLL multilayers, exhibited a remarkable inhibition of the expression of target genes as compared to the use of scrambled siRNA. The gene silencing efficiency depends on the number of siRNA layers within a multilayer. This result indicates that siRNA/PLL multilayers can be potentially utilized for efficient surface-mediated siRNA delivery.