Background Better understanding of the timing and pattern of surveillance bronchoscopy findings after lung transplantation could influence the timing and frequency of surveillance bronchoscopy. We present our surveillance bronchoscopy experience and test the hypothesis that patients not encountering early acute rejection or lymphocytic bronchitis/bronchiolitis are less likely to have subsequent occult occurrences in the 1st year after lung transplantation. Methods We conducted a retrospective study of 204 patients who underword transplantation between 1996 and 2000. Based on contemporary biopsy-specimen grading in the first 100 days, we formed 2 groups: No Early Rejection and Early Rejection. We compared subsequent yields of surveillance bronchoscopy and the incidence of acute rejection or of lymphocytic bronchitis/bronchiolitis. Results We reviewed 645 biopsies taken from 204 recipients during the first 100 days to classify patients into a No Early Rejection Group (n = 67) or an Early Rejection Group (n = 137). Yield of surveillance bronchoscopy for acute rejection or lymphocytic bronchitis/bronchiolitis was 31% with the greatest yield during the first 30 days (45%), and then decreasing to 26% (p < 0.001). After Day 100, 71% of occult acute rejection episodes involved minimal (A1) lesions. Yield of surveillance bronchoscopy after Day 100 was 20% in the No Early Rejection Group and was 27% in the Early Rejection Group (p = 0.22). Incidence of acute rejection or lymphocytic bronchitis/bronchiolitis after Day 100 was 41% in the No Early Rejection Group and was 50% in the Early Rejection Group (p = 0.17). Conclusion Surveillance bronchoscopy detects occult acute rejection or lymphocytic bronchitis/bronchiolitis in approximately one-third of biopsy specimens during the 1st year, with the majority of late abnormalities being minimal (A1) rejection. The absence of acute rejection or lymphocytic bronchitis/bronchiolitis during the first 100 days does not predict freedom from such events in the remainder of the 1st year.