Differences in Mycoplasma hyopneumoniae colonization were evaluated in experimentally inoculated pigs sired by 3 different boars of the same genetic line. Forty-six pigs were used, including a treatment group and positive and negative control groups. The pigs were intratracheally inoculated with an M. hyopneumoniae suspension or with Friis media as a placebo. To evaluate differences in the magnitude of colonization during a 35-day period, nasal and tracheal swabs were collected weekly and tested by nested polymerase chain reaction (N-PCR). Temperature, weight and circulating antibodies were measured for 35 days. At 11 and 35 d postinoculation the pigs were necropsied and macroscopic and microscopic lesions were determined. A section of bronchus was tested by the indirect immunofluorescence test (IFAT), scanning electron microscopy (SEM) and N-PCR. The N-PCR results from the nasal and tracheal swabs showed that the pigs sired by one boar (B3) had a distinctive colonization pattern, different from that of the pigs from the other 2 boars and from the positive controls. SEM studies demonstrated that at 35 d postinoculation a higher proportion of B3 pigs had lower numbers of mycoplasmas attached to the cilia compared with B1 and B2 offspring. No significant differences were observed in temperature and weight gain among groups by ANOVA; however, with use of a 2 x 2 table, temperature differences were observed between pigs sired by boars B1 and B2 at 4 d postinoculation. No pigs seroconverted, showed gross or microscopic lesions, or had positive IFAT results. These results provide evidence of differences in patterns of colonization between pigs sired by different boars, suggesting a possible genetic effect.