Vaginal cytology is a complementary economic method and of simple realization, an indicative to determine in which stage of the estrous cycle the dog is, to achieve a higher fertility and fertility rate. This method is based on determining the type and quantity of cells of the different stages of the estrous cycle, since the hormonal changes that the vaginal mucosa undergoes during the estrous cycle are shown in the morphology of its epithelial cells. The canine female in her reproductive life goes through different phases of activity and hormonal rest that are repeated cyclically. This is called the estrous cycle and consists of 4 stages: proestrus, estrus, diestrus and anestrus. The interpretation of vaginal cytology’s, is a process to which a considerable amount of time is dedicated by its observation in the microscope and the same interpretation by the doctor which can become subjective and poorly performed, causing economic losses for the owners. Therefore, this work proposes an automatic system that will identify six types of cells and the quantity of them in the glass slide, based on a Faster R-CNN to determine in which stage of the estrous cycle the dog is. Our results show an accuracy of 91.6%. The proposed system will improve the efficiency and speed of cytology’s to decreased from 1 h approximately to just a few seconds.