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The objectives of this study were to determine (i) the variation in the bacterial population, (ii) the changes in the number of aerobic bacteria, and (iii) in vitro bacterial susceptibility to different antibiotics after the use of two different intravaginal devices (silicone devices or polyurethane sponges) for 6 or 11 days in goats. During the breeding season, 25 multiparous Saanen goats were randomly allocated to four treatments. Group IS-6 (n = 6) and Group IS-11 (n = 6) goats received a polyurethane intravaginal sponge (60 mg medroxyprogesterone acetate with oxytetracycline in powder) during 6 or 11 days, respectively. Goats from groups SD-6 (n = 7) and SD-11 (n = 6) received an intravaginal silicone device (0.3 g progesterone) during 6 or 11 days, respectively. Before the introduction of the devices, at device withdrawal, and the day of oestrus we performed standard bacteriological procedures on vaginal mucus samples. The predominant bacterial flora at device insertion was gram-positive (77%), and the most frequent strain was Bacilllus sp. The samples obtained on Day 6 [SD-6: 9/12 (75.0%); IS-6: 5/9 (55.5%)] and Day 11 [SD-11: 3/4 (75.0%); IS-11: 5/5 (100%)] were predominantly gram-negative, and the most frequently isolated bacteria was Arcanobacterium pyogenes. The total number of aerobic bacteria forming colony units (CFU/mL) was greater in goats treated with inert silicon device that those treated with intravaginal sponges (P = 0.028). On device removal (Days 6 and 11), we observed more CFU/mL than on device insertion. We observed no difference in CFU/mL on day of oestrus with respect to the day of device insertion (Day 0: 41.1 ± 19.3; Day 6: 187.1 ± 51.3; Day 11: 169.1 ± 27.8; day of oestrus: 20.1 ± 25.8 CFU × 103/mL; P < 0.05). The in vitro studies demonstrated that most samples were resistant to oxytetracycline. We concluded that the use of intravaginal devices, regardless of their composition, provoked an increase in the normal vaginal bacterial flora, but values returned to pre-insertion numbers by the day of oestrus. According to in vitro results, amoxicillin, ampicillin and streptomycin were the most effective antibiotics to prevent vaginal bacterial growth.