Depletion of oocytes from the embryonic ovary is a key feature of mammalian oogenesis; however, the rational and molecular bases for this phenomenon remain poorly understood. Presently in the field, the most systematic analysis used to understand the effect of a given molecular pathway on fetal oocyte attrition is to count the number of oocytes in ovaries at different stages of development. This analysis is commonly done using a sampling method based on sectioning of the ovary, a technique that includes many laborious steps culminating in an inaccurate estimate of oocyte number contained within that ovary. This inability to generate data that are directly comparable between labs hinders the field and raises questions about the timing and rate of oocyte depletion. Therefore, we set out to implement a robust method that can be easily used by most research laboratories to study the dynamics of oogenesis during fetal mouse ovary development in both normal and experimental conditions. Here we describe an approach to accurately count the total number of oocytes in embryonic ovaries. This method is based on whole-mount immunofluorescence, tissue clearing with sucrose and ScaleA2 reagent, and automatic detection and counting of germ cells in intact ovaries using confocal microscopy and three-dimensional software analyses. We demonstrate the power of the method by assessing variation of fetal oocyte numbers between left and right ovaries and between litters of mice. Finally, we anticipate that the method could be adopted to the analysis of substages of meiotic prophase I and ovarian somatic cells.