The objectives of this study were to compare minimally invasive strabismus surgery (MISS) with the fornix approach in paediatric horizontal strabismus surgery (<12 years) and to evaluate early postoperative inflammation, visual acuity and operating time after a four-year training period in MISS. This was a retrospective study of 16 patients (nine male and seven female) with a mean age of 6.75±3.02 years. Bilateral medial rectus surgery was undertaken in nine cases and bilateral lateral rectus surgery for seven cases. MISS procedures were undertaken for 12 right eyes and four left eyes. The fornix approach was used for 12 left eyes and four right eyes. There was no difference between groups for visual acuity outcome. More severe conjunctival hyperemia was noted on postoperative day one for the fornix group (81.3% vs 56.3%) but this was not significant. At the end of follow-up, scars were visible in all cases in the fornix group but only in one case of MISS. There was no significant difference in operative time although MISS took longer (14.43±2.30 vs. 12.37±3.15 minutes). The authors conclude that MISS results are similar to those obtained with the fornix approach but require further larger studies.