The rat whole embryo culture (WEC) system is a suitable experimental tool for the study of the mechanisms of development of the left/right body axis (L/R axis) because embryos can be cultured from before and during the development of several asymmetric structures including the heart. This paper reviews the development of asymmetric structures in rat embryos during the culture period and the literature on abnormal development of the L/R axis studied using the WEC system. In addition, the author suggests the following guideline for investigators who use this system to study the development of the L/R axis. (1) Precisely stage the embryos according to a modified Theiler's system. (2) Examine the sidedness of three asymmetric structures whose sidedness is controlled by different mechanisms [i.e. the heart, chorioallantoic placenta and the lower part of the embryo (the so-called 'tail')]. (3) Establish the background incidences of inversion of the above structures in control groups cultured from different stages. (4) Perform dose-response studies if testing a chemical. (5) Examine antagonists or inactive isoforms to confirm the pharmacological effects of the test chemical.