Milanetto began his career with Juventus in 1993; although he did not make a single appearance for the senior side during the 1993–94 season, he won the 1994 Torneo di Viareggio and the Campionato Nazionale Primavera with the Juventus Youth side. He later played for several different clubs during the following seasons, including Fiorenzuola, Monza (on loan), and Como. In 2000, he joined &lt;a href="Serie%20C1/A"&gt;Serie C1/A&lt;/a&gt; side Modena, and helped the club to achieve successive promotions, eventually making his Serie A debut during the 2002–03 season. Following the retirement of Roberto Baggio in 2004, he joined Serie A club Brescia, where he was re-united with his former Modena coach Gianni De Biasi, although he was unable to save the club from relegation during his first season, spending his second season with the club in Serie B. In 2006, he transferred to Serie B side Genoa, where he remained for five seasons, helping the club to Serie A promotion.