Born at Marostica, a town near Vicenza, the son of Francesco, a physician, Alpini served in his youth for a time in the Milanese army, but in 1574 he went to study medicine at Padua.

After taking his doctor's degree in 1578, he settled as a physician in Campo San Pietro, a small town in the Paduan territory.

But his tastes were botanical and influenced by Melchiorre Guilandino, and to extend his knowledge of exotic plants he travelled to Egypt in 1580 as physician to Giorgio Emo, the Venetian consul in Cairo.

[3] In Egypt he spent three years, and from a practice in the management of datepalms, which he observed in that country, he learned of sexual difference in plants, which was later to become important in the foundation of the Linnaean taxonomy system.

[1] This work introduced a number of plant species previously unknown to European botanists including[5] Abrus, Abelmoschus, Lablab, and Melochia, each of which are native to tropical areas and were cultivated with artificial irrigation in Egypt at the time.

He wrote on the prognosis of diseases in his De praesagienda vita et morti aegrotanti (1601) which led Kurt Sprengel to consider him as a modern father of diagnostic science.