This paper describes a method for investigating clinical process, Layered Analysis, which combines therapist countertransference reports and multi‐faceted microanalytic research approaches. Findings from the application of Layered Analysis to video‐recorded micro‐events of rupture and repair in four psychoanalytic parent–infant psychotherapy sessions are presented. Layered analysis showed that countertransference and observation are complementary perspectives, which enable concomitant study of interactive events, conscious internal experiences, as well as nonconscious and unconscious elements of therapeutic interaction. Interactional rupture and repair were found to constitute co‐constructed micro‐events that occurred fleetingly and often implicitly, and differed in the structure, coherence and flow of interactions and in the relationship between verbal and nonverbal communication. Furthermore, interactional ruptures were found to sometimes ‘get into’ the therapist and transiently disrupt their self‐organization, such that the therapist became a locus of disruption for the patient(s), actively contributing to the rupture, which thus became embedded in the therapeutic system. Interactive repair was found to be most often initiated by the therapist and to be underpinned by the therapist re‐establishing self‐regulation, through metabolizing embodied and verbal aspects of the rupture. Studying such processes can enhance our understanding of clinical process, inform therapist training and clinical supervision, and contribute to clinical outcomes.