Abstract The objective of this study is to examine the expression of Mannheimia haemolytica genes over time during the early stage of infection. In addition, gene expression at different sites of infection in the bovine host was examined. A time-course experiment was designed to collect pharyngeal swabs and lung washings from the same animals over two time points. Six calves were experimentally challenged with M. haemolytica A1; pharyngeal swabs were collected from all animals 5h post infection. Three calves were euthanized at 6h; pharyngeal swabs were collected from the remaining 3 calves at 12h and the calves were euthanized. Lung washings were recovered from all animals at necropsy. Total RNA was prepared from the pharyngeal swabs and lung washings and primers for eight well characterized virulence-associated genes were used in qRT-PCR to examine mRNA levels. The expression of key virulence genes such as lktA, gcp and tbpB was higher in vivo compared to in vitro with the highest changes observed from 6 to 12h. The expression of lktA and gapA increased while expression of fbpA, gs60, nmaA and tbpB was found to decreased over time in the 6h period. Gene expression profiles in the lungs versus the pharynx also differed, with most genes (fbpA, tbpB, nmaA, gs60, lktA and narP) showing higher expressing in lung washings. This is the first study to follow gene expression by M. haemolytica in the same animal over time during an infection.