Abstract Background In the Netherlands, euthanasia or physician-assisted suicide (EAS) is allowed if due care criteria are met. One criterion is consultation of a second independent physician, often SCEN physicians. The public debate about EAS focuses on patients with psychiatric disorders, dementia, and tired of living, as complex cases. What complexities SCEN physicians perceive during consultation is unknown. This study aims to assess the frequency of EAS consultations that are perceived difficult by SCEN physicians, to explore what complexities are perceived by SCEN physicians during consultation, and to assess what characteristics are associated with difficult consultations. Methods Data from 2015 to 2017 from an annual cross-sectional survey among SCEN physicians was used. In 2015, the survey focused on the most difficult consultation that year and in 2016/2017 on the most recent consultation. Frequencies of coded answers to an open-ended question were done to explore what complexities SCEN physicians perceived during their most difficult consultation. Univariable and multivariable logistic regression analyses were used to assess what characteristics were associated with difficult consultations. Results 21.6% of cases consulted by SCEN physicians is perceived difficult. Complexities that SCEN physicians perceive were mainly in contact with patients (79.7%) and in the assessment of due care criteria (41.0%). Characteristics that were associated with a higher likelihood of a consultation being difficult are the attending physician being less certain to perform the EAS, patients staying in the hospital, main diagnosis heart failure/CVA, and accumulation of age-related health problems/psychiatry/dementia, and the presence of a psychiatric disorder, or psychosocial or existential problems besides the main diagnosis. Characteristics that were associated with a lower likelihood of a consultation being difficult are high patient’s age and physical suffering as reason to request EAS. Conclusion Complexities perceived by SCEN physicians in EAS consultations are not limited to the ‘complex’ cases present in the current public debate about EAS, e.g. patients with psychiatric disorders, dementia, and tired of living. Attention for these complexities in intervision could indicate if there is a need among SCEN physicians to enhance knowledge and skills in training and to receive specific support in intervision on these complexities.