Bilharz was born on 23 March, 1825, at Sigmaringen on the Danube, where his father held a position connected with the management of the Royal estates. He was the eldest of nine children, of whom four died young. As a boy he attended the local school, where he displayed exceptional diligence and earnestness in his studies. His love of the study of nature showed itself at an early age, for he was a keen collector of plants, insects and minerals, his tastes in this direction being stimulated by constant access to a collection of natural objects formed by his uncle.