Aim: This study aims to investigate the relationships between cytomorphological markers of pathological processes and the development of acute respiratory infections in children. Materials and Methods: A microbiological study was conducted to identify pathogens based on their morphological, cultural, and biochemical properties using nasopharyngeal swabs. Pure culture isolation and subsequent colonization were performed on standard nutrient media. Cytological studies were carried out using electron microscopy. Results: A total of 114 strains of conditionally pathogenic microorganisms were identified, including 33 strains (29.0%) of Gram-positive bacteria (Streptococcus pyogenes, Staphylococcus aureus, Enterococcus faecalis) and 81 strains (71.0%) of Gram-negative bacteria (Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli). Escherichia coli (37.0%) and Staphylococcus aureus (21.0%) were the predominant pathogens. The study identified key metabolic markers, including sucrose (n=69), maltase (n=87), and lactoperoxidase (n=89), with lactoperoxidase showing the highest levels. Aminoacids and alcohols were analyzed to assess their role in the inflammatory response. Electron microscopy confirmed bacterial localization within epithelial cells and extracellular areas, with morphological signs of epithelial cell destruction, including nuclear degradation and increased vascularization. Conclusions: The findings highlight the significant role of nasopharyngeal microbiota in respiratory infections and their correlation with inflammation markers. The high prevalence of Gram-negative bacteria, particularly Escherichia coli and Staphylococcus aureus, underscores the need for targeted prevention and treatment strategies. Understanding the cytomorphological and biochemical changes in the nasopharyngeal mucosa contributes to a better comprehension of pathogen-host interactions in respiratory infections.