In this case study we present an application of different analytical electron microscopic methods in biology, to elucidate their usefulness in such investigations. Using analytical electron microscopy, spherites in the digestive gland cells of the helicid snail Chilostoma lefeburiana were examined at three stages: just before the non-feeding period of over-wintering in November, in the middle of over-wintering in February and at its end in March. A detailed characterization of changes in the elemental composition of the spherites was characterized by a combination of transmission electron microscopy (TEM), energy dispersive x-ray spectroscopy (EDXS), electron energy-loss spectroscopy (EELS) and energy filtering TEM (EFTEM). During over-wintering, the spherites passed the following changes. Before over-wintering in November, they consisted of striking concentric layers of electron-dense and electron-lucent zones, while in February and March they showed clear empty zones between materials of different electron density. In November spherites, C, O, Ca, P, Cl, Fe, Si, Na, K, Mg and S were detected, whereas in February ones C, O, N, Cl, Si and S were found and only C, O, N, Si and Cl were detected in March spherites. It is suggested that the elements missing in February and March were used in different physiological processes during over-wintering, like (1) the maintenance of the appropriate elemental composition of the internal environment, (2) accumulation of non-toxic waste materials that cannot be metabolized and (3) avoiding potential intoxication by contamination with toxic metals.