Experimental bovine respiratory syncytial virus (BRSV) infection can enhance Histophilus somni (Hs) disease in calves; we thus hypothesized that modified-live virus (MLV) vaccines containing BRSV may alter Hs carriage. Our objective was to determine the effects of an intranasal (IN) trivalent (infectious bovine rhinotracheitis virus [IBRV], parainfluenza-3 virus [PI3V], and BRSV) respiratory vaccine with parenteral (PT) bivalent bovine viral diarrhea virus (BVDV) type I + II vaccine, or a PT pentavalent (BVDV type I and II, IBRV, BRSV, and PI3V) respiratory vaccine, on health, growth, immunity, and nasal pathogen colonization in high-risk beef calves. Calves (n = 525) were received in five truckload blocks and stratified by body weight (213 ± 18.4 kg), sex, and presence of a pre-existing ear-tag. Pens were spatially arranged in sets of three within a block and randomly assigned to treatment with an empty pen between treatment groups consisting of: 1) no MLV respiratory vaccination (CON), 2) IN trivalent MLV respiratory vaccine with PT BVDV type I + II vaccine (INT), or 3) PT pentavalent, MLV respiratory vaccine (INJ). The pen was the experimental unit, with 15 pens/treatment and 11 to 12 calves/pen in this 70-d receiving study. Health, performance, and BRSV, Hs, Mycoplasma bovis (Mb), Mannheimia haemolytica (Mh), and Pasteurella multocida (Pm) level in nasal swabs via rtPCR was determined on days 0, 7, 14, and 28, and BRSV-specific serum neutralizing antibody titer, and serum IFN-γ concentration via ELISA, were evaluated on days 0, 14, 28, 42, 56, and 70. Morbidity (P = 0.83), mortality (P = 0.68) and average daily gain (P ≥ 0.82) did not differ. Serum antibodies against BRSV increased with time (P0.01). There was a treatment × time interaction (P0.01) for Hs detection; on days 14 and 28, INT (21.1% and 57.1%) were more frequently (P0.01) Hs positive than CON (3.6% and 25.3%) or INJ (3.4 % and 8.4%). Also, INT had reduced (P = 0.03) cycle time of Hs positive samples on day 28. No difference (P ≥ 0.17) was found for IFN-γ concentration and Mb, Mh, or Pm detection. The proportion of Mh positive culture from lung specimens differed (P0.01); INT had fewer (0.0%; 0 of 9) Mh positive lungs than INJ (45.5%; 6 of 13) or CON (74.0%; 14 of 19). Vaccination of high-risk calves with MLV did not clearly impact health or growth during the receiving period. However, INT was associated with an altered upper respiratory microbial community in cattle resulting in increased detection and level of Hs.Our objective was to determine the safety, efficiency, and effects on immunity and nasal shedding of respiratory pathogens for high-risk cattle administered an intranasal (IN), trivalent (infectious bovine rhinotracheitis virus [IBRV], parainfluenza-3 virus [PI3V], and bovine respiratory syncytial virus [BRSV]) respiratory vaccine with parenteral, bivalent bovine viral diarrhea virus (BVDV), or a parenteral, pentavalent (BVDV type I and II, IBRV, BRSV, and PI3V) respiratory vaccine, compared to an unvaccinated negative control. The results of this study indicate that modified-live virus (MLV) vaccination of high-risk calves upon arrival, either parenterally or intranasally, did not clearly impact health or growth during the feedlot receiving period. However, cattle that were intranasally vaccinated had increased carriage of Histophilus somni in the naris, greater amount of H. somni in nasal swabs indicated by reduced PCR cycle time, and less frequent culture of Mannheimia haemolytica from lung tissue samples upon necropsy. Therefore, intranasal administration of MLV vaccines may alter the microbial community and balance of opportunistic pathogens in the respiratory tract of cattle.