The physiological mechanisms involved in cardio-respiratory responses to sleep apnea events are not yet fully elucidated. A model-based approach is proposed to analyse the acute desaturation response to obstructive apneas. Methods: An integrated model of cardio-respiratory interactions was proposed and parameters were identified, using an evolutionary algorithm, on a database composed of 107 obstructive apneas acquired from 10 patients (HYPNOS clinical study). Unsupervised clustering was applied to the identified parameters in order to characterize the phenotype of each response to obstructive apneas. Results: A close match was observed between simulated oxygen saturation (SaO 2 ) and experimental SaO 2 in all identifications (median RMSE = 1.3892 %). Two clusters of parameters, associated with different dynamics related to sleep apnea and periodic breathing were obtained. Conclusion and significance: The proposed patient and event-specific model-based analysis provides understanding on specific desaturation patterns, consequent to apnea events, with potential applications for personalized diagnosis and treatment.