We describe a diagnostic software measuring tool (EILOMEA) to objectively describe images obtained by the continuous laryngoscopic exercise (CLE) test, and assess the reproducibility and clinical applications of this tool for the diagnosis of exercise-induced laryngomalacia (EIL) and exercise-induced vocal cord dysfunction (EI-VCD). A total of 97 subjects, 14–24 years of age, were tested with a CLE test. For each laryngoscopic recording, the severity of EIL and/or EI-VCD was assessed by an expert and compared with data obtained using EILOMEA. For both EIL and EI-VCD, a separate objective factor was found describing the degree of laryngeal obstruction by measuring cross-sectional areas of the inspiratory laryngeal images. A threshold value was set giving the diagnosis of EI-VCD, with a sensitivity of 0.65, a specificity of 0.96, a positive-predictive value of 0.79, and a negative-predictive value of 0.93. The threshold set for diagnosing EIL gave sensitivity, specificity, positive and negative-predictive value of 1.00. EIL and EI-VCD show different objective findings confirming that they are two separate conditions both causing laryngeal obstruction. The use of the CLE test is mandatory, because this is the only way to differ between the two conditions and EILOMEA gives the diagnosis and the degree of obstruction objectively.