'autofluorescence' originates from Modern English scientific formation, combining the Greek-derived prefix 'auto-' (from Greek 'autós') meaning 'self' and the word 'fluorescence' (from New Latin 'fluorescens'/'fluorescere'). The element 'fluor-' ultimately relates to Latin 'fluere' meaning 'to flow' (via usage in mineral name 'fluorite').

'autofluorescence' was formed in 20th-century scientific usage by joining 'auto-' + 'fluorescence'. The component 'fluorescence' entered English in the mid-19th century from New Latin 'fluorescens' (from Latin/Neo-Latin formations related to 'fluor-' and the suffix '-escens').

Initially, 'fluorescence' described light emission observed in certain minerals (e.g. fluorite). Over time its use broadened to denote light emission by molecules and biological tissues; 'autofluorescence' later arose to specify fluorescence produced by the object itself without added labels.