Physicochemical characterization is a useful tool in understanding lipoplex assemblies and their correlation to biological activity. Anionic lipid-based ternary siRNA complexes composed of anionic liposomes (DOPG/DOPE), calcium ions and siRNA, have recently been shown to be safe and efficient in a breast cancer cell culture model. In the present work, the effects of various formulation parameters such as liposome composition (DOPG/DOPE ratio) and anionic lipid/Ca2+/siRNA molar charge ratio, on the physicochemical attributes (particle size, surface charge, siRNA loading efficiency and serum stability) of these ternary anionic lipoplexes were evaluated. Particle size, siRNA loading efficiency and serum stability correlated with the in vitro silencing efficiency of these lipoplexes. For example, large lipoplex particles (5/2.5/1 anionic lipid/Ca2+/siRNA molar charge ratio) showed less efficient silencing while absolute serum stability and high siRNA loading (1.3/2.5/1 anionic lipid/Ca2+/siRNA molar charge ratio), exhibited maximum silencing in breast cancer cells. The physicochemical properties also indicated that the siRNA exists in the complexed and/or encapsulated form within the lipoplexes, depending on the anionic lipid/siRNA charge ratio. Based on these studies a model representing lipid-siRNA association within the anionic lipoplexes prepared under various formulation conditions is proposed. Physicochemical attributes can be utilized to estimate in vitro activity of lipid-siRNA complexes and understand their morphology.