Complement activation can be evaluated in vitro using plasma or serum from animals and human donors, and in vivo using animal models. Despite many years of research, there is no harmonized approach for the selection of matrix and animal models. Herein, we present an in vitro study investigating intra- and inter-species variability in the complement activation. We used the liposomal formulation of amphotericin, Ambisome, as a model particle to assess the magnitude of the complement activation in plasma derived from various mouse strains and individual human donors. We demonstrated that mouse strains differ in the magnitude of the complement activation by liposomes and cobra venom factor (CVF) in vitro. Inter-individual variability in complement activation by Ambisome and CVF was also observed when plasma from individual human donors was analyzed. Such variability in both mouse and human plasma could not be explained by the levels of complement regulatory factors H and I. Moreover, even though mouse plasma was less sensitive to the complement activation by CVF than human plasma, it was equally sensitive to the activation by Ambisome. Our study demonstrates the importance of mouse strain selection for in vitro complement activation analysis. It also shows that traditional positive controls (e.g., CVF) are not predictive of the degree of complement activation by nanomedicines. The study also suggests that besides complement inhibitory factors, other elements contribute to the inter- and intra-species variability in complement activation by nanomedicines.