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Mannheimia hemolytica (Mh) and Pasteurella multocida (Pm) strains obtained from bovine nasal discharge of clinically affected by respiratory tract disease calves, were isolated and characterized to estimate the isolation frequency in a dairy complex in the state of Hidalgo, Mexico, over a period of five months by means of a trans-sectional descriptive study. Strains were isolated and typified through selective media and biochemical tests. Chi-square or Fisher’s statistical tests were applied, as well as odds ratio calculation and logistic regression analysis to evaluate the association of some variables on Mh and Pm isolation. Of the 239 calves younger than 1 year of age researched, in 84 (35.14%) Mh or Pm was isolated, 67 (28.03%) of them with Mh and 17 (7.11%) with Pm, in eight calves (3.10%) both microorganisms were isolated. Potential risk factors such as housing, treatment and vaccination were evaluated. The frequency of Mh isolates was higher than the Pm in calf accommodations individual housing or in group housing (P ≤ 0.05); similarly, the frequency of Mh and Pm isolates together were higher in not vaccinated against infectious bovine rhinotracheitis (OR = 2.93, P ≤ 0.05), bovine viral diarrhea (OR = 4.26, P ≤ 0.05), parainfluenza 3 (OR = 2.68, P ≤ 0.05), bovine syncytial virus (OR = 2.36, P ≤ 0.05) and mannheimiosis (OR = 1.97, P ≤ 0.05). Calves housed in the stables and no vaccination against bovine viral diarrhea, were the variables that remained in the logistic regression model. Mh got the highest isolation rate in calf accommodations individual housing or in group housing, as well as in outdoors housing.