Introduction Deep infiltrating endometriosis (DIE) is the most severe form of endometriosis, contributes to pelvic pain syndrome, extragenital symptoms, fertility problems, and diminished reproductive prognosis for affected individuals. It is recommended to use the Endometriosis Fertility Index (EFI) to assess reproductive prognosis and conduct clinical research to compare reproductive prognosis in different forms of endometriosis. Objective Comparison of the impact of the DIE and others forms of endometriosis on EFI, patients' fertility and on reproductive prognosis to understand the management approach. Materials and methods A cohort study included 190 reproductive-age women, divided according to the #Enzian classification: the main group - 85 patients with DIE, the control group - 105 women with other forms of endometriosis. The EFI was utilized for reproductive prognosis. Pain was evaluated with Visual Analog Scale (VAS). Statistical analyses were performed using SPSS, with calculation of the Mann-Whitney U and Pearson's chi-square test (χ²). Results In main group, the frequency of infertility was 83.5% compared to the control group's 71.4% (p > 0.05). The EFI in main group was 7.18±0.25 points vs the control group's 7.13±0.28 points (p = 0.852). Patients in the main group suffered from intense pelvic pain (>7 points by the VAS, p < 0.01), including severe dyspareunia (7.85±0.33 points vs 2.18±0.46 points in control group, p < 0.01). Conclusions Our results suggest that infertility in women with DIE may be more often associated with sexual abstinence due to significant dyspareunia rather than organic impairments. Thus, EFI in patients with DIE does not reflect all aspects of infertility and has reservations, and consideration of both physical symptoms and sexual health is crucial in managing DIE to optimize fertility outcomes. These findings open the way to the feasibility of surgical treatment of DIE to improve sexual quality of life, which will reduce the need for IVF and increase the chances of spontaneous pregnancy in patients, but this conclusion requires further investigation in randomized clinical trials.