Purpose YKL-40 is a chitinase-like protein involved in the innate immune response to chitin containing organisms. Dysregulation of YKL-40 is seen with numerous human diseases characterized by inflammation and tissue remodeling including airway remodeling in asthma. In a small exploratory study, we found that YKL-40 transcription during Aspergillus colonization was associated with the future development of BOS. We sought to validate the relationship of YKL-40 with Aspergillus and BOS in a larger longitudinal study after lung transplantation. Methods and Materials We performed a retrospective study of adult lung transplant recipients from 2000-2008 with at least one available bronchoalveolar lavage fluid (BALF) specimen. YKL-40 protein concentrations were determined in BALF specimens using the MicroVue YKL-40 EIA Kit (Quidel) according to manufacturer instructions. Given that YKL-40 was repeatedly measured over time within a patient, we fit a random effects generalized linear model to investigate the effects of Aspergillus and other covariates on YKL-40 over time. Results We assayed 750 BALF samples from 204 lung transplant recipients. Aspergillus colonization was associated with a higher BALF concentration of YKL-40. YKL-40 concentrations were also significantly elevated after a diagnosis of BOS. YKL-40 concentrations were not significantly affected by acute rejection. Conclusions In a large longitudinal cohort of lung transplant recipients, YKL-40 production in the lung is increased during Aspergillus colonization and after BOS, validating transcriptional profiles in a smaller exploratory study. YKL-40 may play a role in a continuum of pathogenesis from Aspergillus colonization to BOS. Factors Influencing BALF YKL-40 Concentration Estimate Standard Error P value Intercept 144.81 14.69 Log months to BAL -14.23 2.81 Acute cellular rejection (A2 or greater) 12.23 8.54 0.15 BOS at time of sample collection 53.32 9.96 Aspergillus colonization 25.39 8.78 0.004