The impact of patient-physician communication and levels of understanding of treatment on patient knowledge and compliance has been studied in patients undergoing their first cycle of infertility treatment. This observational, real-life, longitudinal study involved 488 patients from 28 infertility centres in France. Data on communication quality, understanding of treatment instructions, patient knowledge and compliance to treatment protocol were collected through questionnaires administered before treatment initiation (V1) and at oocyte retrieval (V2). At V1, patients were very satisfied with their levels of understanding of the injection and monitoring schedules, the information given by the medical team, and the way of receiving instructions, with average ratings on a scale of 0-100% of > 75%. They rated their understanding of possible treatment side-effects as satisfactory (average score 71.1%). Gaps in patient knowledge about their treatment, revealed by discrepancies between physician and patient reports, were observed in 20.5% of patients (n = 79/386), and most commonly resulted from confusion about the units and dose of gonadotropin. Anxiety about performing self-injections and a lack of confidence in their ability to self-inject correctly were each observed in approximately one-third of patients. Patient self-assessment of compliance at V2 revealed that 27% of patients (n = 83/305) did not comply with or had doubts about the injection schedule or dose injected. Meanwhile physicians reported high levels of patient compliance (94.3%; n = 350/371). In conclusion, even when patient-physician relationships appear to be satisfactory, patient miscomprehension and non-compliance during infertility treatment may be underestimated. Further interventions are required to improve these outcomes.