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ABSTRACT Bovine respiratory diseases are widespread and present a multifactorial and variable etiology. However, several aspects of their origin remain understudied. Therefore, the objective of the present study was to investigate the effect of changes in calves’ keeping conditions on their clinical state in terms of microbiocenosis in their respiratory tract. The study was conducted in the winter season, with 37 healthy calves, 5-6 months in age, which were transferred from calf barn number 1 with favorable conditions to calf barn number 2 having a similar design as that of the previous barn but with unfavorable microclimatic parameters (drafts, low temperature, and high humidity). Within 7-9 days after their transfer to the other barn by a veterinary specialist, 54.1% of the calves were diagnosed with catarrhal bronchopneumonia. On day 10, all animals were slaughtered and dissected. Mucus samples for bacteriological analysis were obtained from the mucous membrane of seven sections of the respiratory tract of animals. In all calves, the highest degree of contamination was observed in the first half of the ventral nasal passage (84.9 ±24.46% in healthy calves and 85.7 ±18.55% in sick calves). In healthy calves, the degree of contamination in the front of the choanae was lower by a factor of 56.2% (P = 0.000059) compared to sick calves, and this value continued to decrease when moving toward the lower respiratory tract until the complete disappearance of the bacteria.