Selective breeding practices have impacted the intra-breed genetic diversity of Chihuahuas, increasing homozygosity for deleterious alleles and predisposing the breed to specific hereditary conditions. Although DNA sequencing represents the golden standard for genetic diagnosis, its cost and technical requirements limit its widespread use in routine veterinary practice. This study developed comprehensive and cost-effective Polymerase Chain Reaction-Re-striction Fragment Length Polymorphism (PCR-RFLP) methods to screen for Mendelian genetic disorders in Chihuahuas. Using the Online Mendelian Inheritance in Animals (OMIA) database and reference genomic sequences, specific primer-enzyme sets were designed for nine genetic variants associated with eight disorders: ichthyosis (ALOXE3 and SDR9C7), epidermolytic hyperkeratosis (KRT10), Ehlers-Danlos syndrome (COL5A2), verrucous epidermal keratinocytic nevi (NSDHL), methaemoglobinaemia (CYB5R3), Alexander disease (GFAP), progressive rod-cone degeneration (PRCD), and spinal dysraphism (NKX2-8). Predicted electrophoresis profiles confirmed that the selected enzymes generate distinct digestion patterns, enabling the clear differentiation of homozygous wild-type, heterozygous, and homozygous mutant genotypes. These protocols offer a robust, rapid, and economical alternative to sequencing for identifying carriers and affected individuals. The integration of these methods into clinical diagnostics and breeding programs provides a practical tool for facilitating informed breeding decisions.