Most surgeons recommend the use of full thickness skin grafts (FTSGs) for syndactyly repair in order to achieve a tension free reconstruction and prevent web creep. The inguinal region, cubital fossa and wrist are all well recognised donor sites for such FTSGs but unfortunately often result in visible scars. Furthermore, the inguinal graft has the potential to develop hair growth at the onset of puberty. An alternative donor site is the retroauricular skin. This retrospective study is the first to compare the functional outcome, aesthetic result, and parental satisfaction arising from retroauricular and inguinal FTSGs. Evaluation was based on visual assessments using the ‘Pantone Skin Tone Guide’ (PSTG) and the ‘Patient and Observer Scar Assessment Scale’ (POSAS). Results suggested that the use of retroauricular FTSGs gave a better result for syndactyly repair on the hand than inguinal FTSGs. Retroauricular FTSGs produced a significantly better pigmentation match and resulted in significantly higher parents’ and observers’ overall impression of the donor site. There was no significant difference in parent satisfaction. Recipient site complication rates were similar for both techniques. The study concludes that, retroauricular FTSGs present a good alternative to inguinal FTSGs in syndactyly repair, however, multiple complex syndactylies may still warrant the use of inguinal FTSGs due to limitation of graft size at the retroauricular site.