'autonephrectomy' originates from Greek and New Latin elements: 'auto-' (from Greek 'autos') meaning 'self' and 'nephrectomy' (from Greek 'nephros' + 'ektomē') meaning 'kidney excision'.

'nephrectomy' changed from Greek 'nephros' (kidney) + 'ektomē' (excision) into New Latin/medical Latin as 'nephrectomia' and entered English as 'nephrectomy'; the modern compound 'autonephrectomy' was formed in medical English by adding the prefix 'auto-' to indicate 'self' or 'self-caused'.

Initially the components meant 'self' and 'kidney excision'; over time the compound came to be used to describe a kidney destroyed or rendered nonfunctional by disease so that it is effectively 'self-removed' (i.e., functionally equivalent to surgical nephrectomy).