This paper describes the use of Atomic Force Microscopy (AFM) to investigate the plasma membrane of Xenopus laevis oocyte. Different protocols of sample preparation to perform an AFM investigation of both external and intracellular sides of the oocyte plasma membrane are presented and discussed. Reproducible AFM images allowed visualization and dimensional characterization of protein complexes differently arranged on both sides of the oocyte plasma membrane. In particular, two different arrangements were visualized: (1) a heterogeneous and irregular distribution of the protein complexes and (2) in some cases a distribution of nanometer-sized membrane domains where protein complexes are densely packed and spatially arranged in an ordered hexagonal motif. In addition, a methodological approach based on the purification of oocyte plasma membrane by ultracentrifugation on sucrose gradient is also described in this work. The potential of AFM as a useful tool for the structural characterization of proteins in a native eukaryotic membrane was established and its relevance for describing the organization of protein complexes in native biological membranes was explored.