The Italy striker has scored four of Milan's seven goals since the arrival of Clarence Seedorf as coach in January, but a shoulder injury will force him to miss the trip to the Luigi Ferraris.
Balotelli picked up the problem in Wednesday's 1-0 defeat to Atletico Madrid in the first leg of the sides' UEFA Champions League last-16 tie.
Seedorf's appointment has improved the domestic form of Milan, who have lost just one of five Serie A games since the Dutchman replaced Massimiliano Allegri.
However, their faint hopes of securing European football with a top-five finish could well suffer a blow at a stadium where the 18-time champions have struggled to earn positive results.
Indeed, Milan have not won a league game at Sampdoria since October 2007, Seedorf scoring the final goal in an emphatic 5-0 win on that day.
Injuries at both ends of the pitch may hamper Milan's chances of ending that run, with Mattia De Sciglio (ankle) also having picked up an injury in midweek.
The absence of the right-back and Balotelli will come as a blow to a side already missing several first-team players, including strikers Robinho (thigh) and Stephan El Shaarawy (foot).
Valter Birsa (hamstring), Bryan Cristante (leg) and Matias Silvestre (calf) are also unavailable for Milan, while the suspended pair of defender Daniele Gastaldello and midfielder Lorenzo Di Silvestri miss out for Samp.
Striker Maxi Lopez, scorer of the winning goal in the derby against fierce rivals Genoa earlier this month, is nearing a return from a foot injury, but Gianluca Sansone is a doubt through illness.
Samp were hammered 3-0 by Roma last weekend but are nine points clear of the drop zone despite an inconsistent campaign.
The appointment of Sinisa Mihajlovic in November has proved key to Samp's improving prospects of staying in the top tier, with the Serbian overseeing a handy revival following a dismal start to the campaign under Delio Rossi.
Samp won only two of their first 12 Serie A games this season, but have since claimed victory in five of the next 12 following Mihajlovic's appointment.
Despite their relatively strong form, midfielder Angelo Palombo does not believe Samp can afford to ease off in the closing stages of the season.
"We have to raise our level again on Sunday and return to speed as soon as possible," Palombo said. "Because with 28 points we cannot be relaxed."
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