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Objectives: Vaginal and endocervical infections are considered a global health problem, especially after recent evidence of their association with preterm delivery and other adverse obstetric outcomes. Still, there is no consensus on the efficacy of a screening strategy for these infections in the first trimester of pregnancy. This study evaluated their prevalence and whether screening and treatment resulted as effective in reducing pregnancy and perinatal complications. Methods: A single-center prospective observational study was designed; a sample size of 400 first-trimester pregnant women was established and they were recruited between March 2016–October 2019 at the Puerta de Hierro University Hospital (Spain). They were screened for vaginal and endocervical infections and treated in case of abnormal flora. Pregnancy and delivery outcomes were compared between abnormal and normal flora groups by univariate analysis. Results: 109 patients had an abnormal flora result (27.2%). The most frequently detected infection was Ureaplasma urealyticum (12.3%), followed by Candida spp. (11.8%), bacterial vaginosis (5%), Mycoplasma hominis (1.2%) and Trichomonas vaginalis (0.8%). Patients with abnormal flora had a 5-fold increased risk of preterm premature rupture of membranes (5.3% vs. 1.1% of patients with normal flora, Odds Ratio 5.11, 95% Confidence Interval 1.20–21.71, p = 0.028). No significant differences were observed regarding preterm delivery or neonatal morbidity. Conclusions: Considering the morbimortality related to prematurity and that the results of our study suggest that the early treatment of abnormal flora could improve perinatal outcomes, the implementation of a screening program during the first trimester should be considered.