Reptiles are potential reservoirs of bacteria that could be transmitted, thus becoming a zoonotic hazard. (1) Background: This three-year investigation surveyed the pathological status of 398 pet reptiles: chelonians, snakes (venomous/non-venomous), and lizards. The main pathological entities found were related to the skin, the sensory organs, the digestive system, the respiratory system, the cardiovascular system, the urinary system, the genitalia, the osteo–muscular tract, surgical issues, tumors, and intoxications. (2) Methods: In 25 individuals treated with antibiotics, no clinical healing was recorded, for this reason, an antimicrobial resistance profile analysis of the 43 samples gathered was processed. An antibiogram was performed using the VITEK®2 ID-GP (bio-Mérieux, Marcy l’Etoile, France) automated platform, with 22 bacterial strains being isolated. (3) Results: The statistics (ANOVA) revealed that the most common disease category was diseases of the digestive system, followed by diseases of the skin, respiratory system, nervous system, and reproductive system. A significant correlation (p < 0.01) between disease incidence and reptile species was reported, with correlations found between all species and diseases diagnosed. The most common bacteria isolated were Enterococcus faecalis, Pseudomonas aeruginosa, Stenotrophomas (Xanthomonas) maltophilia, Escherichia coli, Klebsiella oxytoca, and Salmonella spp., but Beta-hemolytic Streptococcus, Staphylococcus aureus, Citrobacter spp., and Proteus spp. were also identified. (4) Conclusions: These microorganisms revealed degrees of resistance against penicillins, cephalosporins, macrolides, lincosamides, aminoglycosides, and tetracyclines. The animals can be categorized according to their sensitivity to diseases in the following order (most sensitive to least sensitive): chelonians, venomous snakes, non-venomous snakes, and lizards.