However, after a trail of injuries, Zidan was on the receiving end of less playing time. After months of speculations, following the limited playing time and injuries, Werder Bremen announced on 16 January 2007 that Zidan would be transferred to Mainz for a reported 2.8 million Euros fee, which made it the largest ever purchase in the club's history, passing his medical on 17 January 2007. He scored six goals in the first 5 matches with his new club, catapulting the team from last, to 10th place on 1 March 2007 with 27 points. The Egyptian talent also received 50% of votes by the Kicker magazine, and earned himself the title of "Player of the month" in February in Germany, while Mainz became "Team of the Month" in the German Bundesliga.
During the 2007 season Zidan contributed many spectacular goals, but could not save Mainz from relegation. The club had only been able to score 34 goals in the entire season, 13 of which, despite having played for less than half of a season, came from the Egyptian forward's feet. Unfortunately Zidan's hard-work and valuable solo contribution was insufficient to prevent Mainz from the depths of despair of being relegated to the second division. However, Zidan's work was noticed by number of top established clubs based in Spain, France and England as well as German champions VfB Stuttgart.
On 3 June 2007, Zidan passed a medical and thereby completed his move to HSV. He said that he always wanted a move to the north-German club, because he still has many ties to Denmark. The transfer fee was suspected to be about €5.8 million.