A longitudinal study was conducted in pigs to evaluate the effect of nutrition and use of antibiotics for weaner pigs on ileal bacterial microbiota. Forty-eight pigs were weaned at 21 ± 2 d of age and fed a high complexity diet (High) or low complexity diet (Low) with chlortetracycline (A+) or without chlortetracycline (A-) for 6 wk. All pigs received the same grower diet thereafter. Pigs were killed at week 2, 4, and 8 and ileal digesta as well as a 40-cm section of the distal ileum were taken for extraction of digesta and mucosa-associated bacteria, respectively. Total DNA was extracted using a commercially available kit and PCR amplicons were generated using HDA1-GC and HDA2 primers against the V3 region of the 16S rRNA gene. Denaturing gradient gel electrophoresis (DGGE) of PCR amplicons was used for separation of distinct bacteria communities. Similarities of PCR-DGGE profiles were analyzed with Bionumerics software and the degree of similarity represented by a similarity coefficient. The DNA bands were compared using a positional tolerance of 0.5%. In the digesta, HighA-, LowA+, and LowA- were 47.6, 63.6, and 58.8% similar, respectively, at week 2 and 64.0, 69.2, and 66.7% similar, respectively, at week 4. Digesta bacteria were 90.9 (HighA-) and 85.7% (LowA-) similar to HighA+ at week 8 but due to a smiling edge of the DGGE gel, the profile for LowA+ was deemed inappropriate for similarity analysis. In the mucosa, HighA-, LowA+, and LowA- were 58.8, 80.0 and 44.4% similar, respectively, compared to HighA+ at week 2; 81.5, 75.0, and 88.9% similar, respectively, at week 4; and 81.8, 76.2, and 78.3% similar, respectively, at week 8. The bacterial profile was more similar between weeks 2 and 4 in the digesta than in the mucosa but more similar between weeks 4 and 8 in the mucosa than in the digesta. Postweaning nutrition may have a long-term effect on ileal mucosa-associated--but not ileal digesta--microbiota profiles.