This retrospective study aimed to investigate the impact of microorganisms identified in the reproductive tract on disorders during the early adaptation period in newborns. A cohort of 823 patients and cervical canal cultures were analyzed to identify the presence of microorganisms. Newborns included in the study were divided into two groups due to the number of pathogens identified in the swab from the cervical canal of the mother. The first group consisted of newborns whose mothers had one pathogen identified (N = 637), while the second group consisted of newborns whose mothers had two or more pathogens identified (N = 186). The analysis of disorders of the early adaptation period included the incidence of respiratory distress syndrome, the number of procedures performed with the use of CPAP, oxygen therapy, antibiotic therapy and parenteral nutrition. Respiratory distress syndrome was more common in group II than in group I (85 vs. 31, p = 0.001). In group II, CPAP (63 vs. 21, p = 0.001), oxygen therapy (15 vs. 8, p = 0.02) and antibiotics were used more frequently (13 vs. 8, p = 0.01). The findings of this study revealed that the number of pathogens colonizing the reproductive tract had a significant influence on the early adaptation period in newborns. Multifactorial colonization of the reproductive tract was associated with an increased incidence of infections in newborns and a higher prevalence of acid-base balance disorders. This study highlights the importance of monitoring and addressing the microbial composition of the reproductive tract during pregnancy.