Infections of the genitourinary tract are one of the most frequent causes of diseases that affect dogs and cats, and is usually from bacterial origin because the urinary tract is considered a sterile environment (except the distal urethra). Thus, the aim of this study was to survey the cases of genitourinary infections which affected dogs and cats between August 2004 to December 2015. For the purpose of identify the main bacterial species and their antimicrobial resistance profile which affected the animals treated at the Veterinary Clinical Hospital UDESC. This study showed an increase of tests requested over the years, being that the number of urine samples and vaginal swabs in the years 2005 to 2012 corresponded to 23.4% (120/513), while the years 2013, 2014 and 2015 corresponded to 23.2%(119), 23.4%(120) and 30%(154) respectively. A total of the 513 samples, 69.6%(357) were from dogs and 20.4% (156) from cats, and 232(45.2%) showed no growth, 27.1%(139) were isolated Gram positive bacteria and 27.7%(142) Gram negative, where the major microorganisms were E. coli with 26.3%(74/281) and Staphylococcus sp. 25.6%(72) followed by Streptococcus sp. (60 - 21.5%) and Proteus sp. (22 - 7.8%). The antimicrobial susceptibility test was performed according to the availability of antibiotics in the laboratory, with different classes used over the years. Antimicrobials tested more frequently were: enrofloxacin (260), norfloxacin (254), ciprofloxacin (242), florfenicol (241), ampicillin (216), amoxicillin (209), amikacin (205), cephalexin (202) and ceftriaxone (192), and ampicillin, amoxicillin and cephalexin those with the highest resistance, 50.46%, 46.41% and 35.64%, respectively. Already amikacin (16.59%), florfenicol (18.67%) and ceftriaxone (22.4%) showed less resistance. Fluoroquinolones, highly utilized in genitourinary infections, showed 27.95%(norfloxacin), 29.34% (ciprofloxacin) and 31.54% (enrofloxacin). Antimicrobials with higher resistance were: sulfonamide with 77.55% (38/49), streptomycin 74.55% (41/55) and tetracilcina 60.38% (32/53). The correct choice of treatment for infections affecting small animals is only possible with the identification and susceptibility testing to antimicrobial, since the use of these drugs incorrectly can lead to the emergence of multidrug-resistant microorganisms and eventually hamper treatment infections considered simple.