Abstract Objective—To determine the prevalence of Mycoplasma bovis infection in the lungs of cattle at various times after arrival at a feedlot, to measure the relationship between clinical disease status and the concentration and genotype of M bovis within the lungs, and to investigate changes in the genotype of M bovis over time. Sample—Bronchoalveolar lavage fluid (BALF) from 328 healthy or pneumonic beef cattle and 20 M bovis isolates obtained from postmortem samples. Procedures—The concentration of M bovis in BALF was determined via real-time PCR assays, and M bovis isolates from BALF were genotyped via amplified fragment length polymorphism (AFLP) analysis. Results—Prevalence of M bovis in BALF was 1 of 60 (1.7%) at arrival to a feedlot and 26 of 36 (72.2%) and 36 of 42 (85.7%) at ≤ 15 days and 55 days after arrival, respectively. Neither the concentration nor the AFLP type of M bovis in BALF was correlated with clinical disease status. The M bovis AFLP type differed between early and later sampling periods in 14 of 17 cattle. Conclusions and Clinical Relevance—The findings implied spread of M bovis among calves and suggested that host factors and copathogens may determine disease outcomes in infected calves. Chronic pulmonary infection with M bovis may represent a dynamic situation of bacterial clearance and reinfection with strains of different AFLP type, rather than continuous infection with a single clone. These findings impact our understanding of why cattle with chronic pneumonia and polyarthritis syndrome inadequately respond to antimicrobial treatment.