In Europe, there is a growing concern for animal welfare, encompassing both their rights and health. Consequently, identifying biomarkers that predict serious pathological conditions has become crucial in veterinary medicine. The Buccal Micronucleus Cytome (BMCyt) assay is a minimally invasive method that uses biomarkers to evaluate DNA damage and chromosomal instability, using exfoliated buccal cells. A rising frequency of anomalies, such as micronuclei formation, strongly indicates an elevated risk of cancer, neurodegenerative diseases, or accelerated aging, potentially originating from exposure to genotoxins and cytotoxins. This method has been validated in humans, but very little research has been conducted on animals. This work aims to provide a detailed description of an optimized method for collecting buccal exfoliated cells in dogs and to characterize a biomarker related to genomic damage using optical and fluorescent microscopy. Samples from dogs in breeding kennels, including pregnant animals, were tested for chromosomal instability. By following procedures similar to those used in humans, we were able to detect and count major nuclear abnormalities. The percentage of micronuclei was higher compared to other studies. Technical aspects, such as avoiding artifacts and ensuring prior training of the operator, must be taken into account. This work validated the BMCyt method for collecting and processing samples in dogs, potentially enhancing the understanding of micronuclei as biomarkers for pre-pathological states in canines.