'bacillophobia' originates from New Latin and Ancient Greek, specifically the New Latin 'bacillus' and the Greek word 'phóbos' (φόβος), where 'bacillus' meant 'little rod' (diminutive of Latin 'baculum', 'staff/rod') and 'phóbos' meant 'fear'.

'bacillus' came into New Latin from Latin 'bacillum' (diminutive of 'baculum'), meaning 'little rod'; the combining form '-phobia' comes from Greek 'phobos'. These elements were combined in modern English coinage to form 'bacillophobia'.

Initially the components referred literally to 'fear of little rods' (bacilli); over time the compound came to mean the modern medical/psychological concept 'fear of bacteria or germs' more generally.