Background Minimally invasive surgery (MIS) is not without impact on surgeons’ neck/shoulder/head and eyes. However, the mechanisms for concurrent symptoms are not clear. This study aims to examine the effect of visual impairments on physical symptoms and surgical performance among surgeons performing simulated surgical tasks using two-dimensional (2D) and three-dimensional (3D) viewing modes. Methods Gynaecologists with experience in laparoscopy performed four simulated surgical tasks in the 2D and 3D viewing modes. Visual parameters (accommodation, convergence and stereoacuity) were measured prior to commencement. Objective performance measures were derived from the laparoscopic tasks, and surgeons also self-reported their mental and physical workload using the NASA-TLX. In addition, perceived symptoms were measured using Visual Analogue Scales, the Simulator Sickness Questionnaire and the Computer Vision Syndrome Questionnaire. Results Seventeen healthy gynaecologists participated in this study. There were significant relationships between visual impairments and both the perceived symptoms and surgical performance scores of MIS surgeons. Surgeons with a higher number of accommodation/convergence dysfunctions and/or poorer stereoacuity tended to have poorer objective performance scores on simulated surgical tasks in both viewing modes. NASA-TLX scores indicated that surgeons with poorer stereoacuity also perceived themselves to have been less successful at accomplishing tasks. However, these surgeons also reported less intense physical symptoms and simulator sickness. Conclusions Surgeons’ performance for the simulated surgical tasks correlated with visual functions, and it also impacted on the symptoms experienced. Regular screening of surgeons’ vision and vision therapy may be required to decrease physical symptoms and improve surgical performance.