In the present study, the morphological variations in the isthmus segment of goat (Capra hircus) oviduct were studied using scanning and ultrastructural techniques during luteal and follicular phases of oestrous cycle. Topographic analysis of the isthmus epithelium in the follicular phase demonstrated irregular distribution of ciliated cells on the epithelium. A few secretory cells possessed bulbous apical processes which were concealed by the cilia. Cyclic changes were noticed in the secretory cells of isthmus. Under electron microscopy the isthmus region of the oviduct during the follicular phase revealed presence of almost blunt processes at their apical surfaces. The secretory cells were attached to the basal lamina and were characterized by the presence of secretory granules, numerous ribosomes, extensive smooth endoplasmic reticulum, well-developed golgi zones in the cytoplasm, and a microvillus luminal surface. The parallel use of these two methods in isthmus segment of the oviduct has enabled us to analyze the marked cyclic variations in the topography and fine structure during follicular and luteal phases of the oestrous cycle. The results of the present investigation on topography and ultrastructure will be of great help in explaining different bottlenecks of gamete interaction, maturation, fertilization, and early embryo development. SCANNING 35:344-348, 2013. © 2013 Wiley Periodicals, Inc.