Lung sounds provide useful information for assessing and monitoring respiratory patients, but standard auscultation is subjective. Computer aided lung sound analysis (CALSA) enables the quantification and characterisation of added lung sounds (e.g. crackles). At present, little is known about the reliability of these sound characteristics. Therefore, the aim of this study was to explore the reliability of crackle initial deflection width (IDW) and two-cycle deflection (2CD) in a clinical population. Fifty-four subjects (37 bronchiectasis, 17 cystic fibrosis) were recruited from out-patient clinics. Three repeated lung sound recordings were taken at seven anatomical sites with a digital stethoscope connected to a laptop computer. The intra-subject reliability of crackle IDW and 2CD was found to be 'good' to 'excellent', estimated by the analysis of variance, intraclass correlation coefficient (IDW 0.76;0.85, 2CD 0.83;0.94), Bland and Altman 95% limits of agreement (IDW -0.50;0.47 ms, 2CD -2.12;1.87 ms) and smallest real difference (IDW 0.30;0.66 ms, 2CD 1.57;2.42 ms). Crackle 2CD was found to be more reliable than IDW. It is concluded that crackle IDW and 2CD characterized by CALSA have good test-retest reliability. This technique requires further evaluation since CALSA has potential to diagnose or monitor respiratory conditions, and provide an objective physiological measure for respiratory interventions.