Abstract Background Mentoring plays a pivotal role in workplace-based learning, especially in the medical realm. Organising a formal mentoring programme can be labor and time intensive and generally impractical in resource constrained medical schools with limited numbers of mentors. Hence, informal mentoring offers a valuable alternative, but will be more likely to be effective when mentors and protégés share similar views. It is therefore important to gain more insight into factors influencing perceptions of informal mentoring. This study aims to explore mentors and protégés’ perceptions of informal mentoring and how these vary (or not) with gender, age and the duration of the relationship. Method We administered an Informal Mentor Role Instrument (IMRI) to medical practitioners and academics from Egypt, Pakistan and Saudi Arabia. The questionnaire was developed for the study from other validated instruments. It contained 39 items grouped into 7 domains: acceptance, counselling, friendship, parenting, psychological support, role modelling and sociability. Results A total of 103 mentors and 91 protégés completed the IMRI. Mentors had a better appreciation for the interpersonal aspects of informal mentoring than protégés, especially regarding acceptance, counselling and friendship. Moreover, being older and engaged in a longer mentoring relationship contributed to more positive perceptions of interpersonal aspects of mentoring, regardless of one’s role (mentor or protégé). Conclusion It can be concluded that the expectations of mentors and protégés differed regarding the content and aim of the interpersonal characteristics of their mentoring relationship. We recommend mentors and protégés to more explicitly exchange their expectations of the informal mentoring relationship, as typically practiced in formal mentoring. Additionally, in our study, seniority and lasting relationships seem crucial for good informal mentoring. It appears beneficial to foster lasting informal mentoring relationships and to give more guidance to younger mentors.