Background Many patients suffer from incisional hernia all over the world. Although various surgical techniques have been introduced in recent decades, the occurrence of this problem still remains as a challenge facing surgeons. Objectives To compare the modified sandwich technique (MST) to on-lay mesh repair technique (OMR) in the repair of huge incisional hernias. Patients and Methods In a randomized control clinical trial during 2004–2008 in Shiraz, Southern Iran, 90 patients with huge incisional hernias were randomly approached by two repair techniques namely MST and OMR. In MST group, polypropylene mesh was fixed in each side of fascia with nylon 2-0 and the wound closure was done with nylon loop 1 , while In OMR technique, the fascia was released 5 cm in each side and polypropylene mesh was fixed with nylon 2-0. The wound closure was identical to MST group. Results The mean age of patients in MST group was 49.3 years with a standard deviation (SD) of 11.8 years and 48 years with SD of 13.6 in OMR group. Recurrences occurred primarily during the first two postoperative years in both groups. Total recurrence rate following MST procedure was 2.2%, compared to 18.2% for OMR (P = 0.01). Mean of hospitalization was 3.4 days in MST group and 4 days in OMR (P = 0.6). The percentage of female patients was 69.6% in MST group and 77.3% in OMR. Mean operation time was 2.3 hours in MST comparing to 2.1 hours in OMR (P = 0.7). Conclusions Our results showed that in the repair of incisional hernias, MST led to a lower recurrence rate and fewer major complications in comparison to OMR.