Background Early differentiation of rattling infants, frequently misdiagnosed as wheezing, is important to prevent under- and overtreatment. Exhaled breath biomarkers reflect metabolic processes and can potentially aid differential diagnosis. This study investigated the potential of exhaled biomarkers in differentiating rattling infants. Methods Exhaled breath collected from infants (2-18months) with an adjusted breath sampler was analysed using gas chromatography mass spectrometry (GC-MS) and selected ion flow tube mass spectrometry (SIFT-MS). Linear discriminant analysis was used to classify recovered, mild, moderate and severe rattling infants in a one-vs-all approach. The potential of parent reported outcome about symptoms and burden to improve the discriminant models was also investigated. Results Classifying the diagnostic groups (recovered, mild, moderate, severe rattling) based on exhaled breath showed potential with accuracies between 69.12-75.0% for GC-MS and 59.21-69.74% for SIFT-MS. Highest accuracy and specificity was achieved for severe rattling vs all other diagnostic groups. Adding parent reported symptoms in past the three days to the discriminant model increased accuracies (69.12-86.76% GC-MS; 65.79-88.16% SIFT-MS), particularly for moderate and severe rattling infants. The differentiating VOCs were of the type alkane, acids, amine, imine, triazine and ketone. Conclusion Exhaled breath analysis has potential to differentiate infants with different rattling severities and recovered infants. Additionally, combining parent reported symptoms in the past three days with exhaled breath biomarkers improved the performance of the diagnostic models.