Postoperative behaviour and changes in the structure of free microvascular muscle flaps are unknown. Magnetic resonance imaging was used to monitor postoperative structural changes in free muscle flaps. MRI was conducted on 10 patients 2 weeks and 6 months postoperatively. The results were correlated with our earlier findings using ultrasonography and computed tomography. Oedema and fat degeneration were visually assessed (scale 1–4) and T2-dependent signal intensity, flap thickness and volume were measured from the MR images. When the 2 weeks values were compared with the 6 month's ones it was found that intramuscular oedema decreased from 3±0.5 (moderate) to 1.7±0.5 (slight) (p<0.05) and fat degeneration increased from 1.1±0.33 (normal) to 1.9±0.78 (slight) (p<0.05). T2-weighted signal intensity, representing postoperative inflammatory changes, oedema, and also reflecting changes induced by denervation, declined by 28%. The volume of the free flap increased by a mean of twice (from 162±81 ml to 305±135 ml) the initial values in a 2 week period (p<0.05), and attained its initial volume in 6 months (132±69 ml). The thickness of the transplant increased from 11.8±2 mm to 24±4 mm in 2 weeks (p<0.05) and decreased to 13.8±3.5 mm at 6 months. MRI also shows that a free microvascular muscle tightly fills cavities. The correlation between MRI and earlier US studies was 0.71 and between MRI and CT 0.83. MRI is an accurate but expensive research tool to evaluate noninvasively changes in free muscle flaps after the surgical procedure. A 6-month follow up, this study showed that after extensive postoperative swelling the flap attains its initial thickness. The structure of the free flap changes: muscle is replaced by fatty degeneration and also the surface of the flap becomes thicker. Signs indicating denervation induced intramuscular changes in the flap were also noted.