Barry Bonds and Albert Pujols have both made headlines with their home runs lately, and in the coming months, their fates may become even more intertwined. This week’s three game series between the Giants and Cardinals offered a fascinating juxtaposition between two of baseball’s most accomplished sluggers, and a potential changing of the guard.

In the home dugout was Bonds. Diminished by injuries and surrounded by controversy, the 41-year-old Giants’ leftfielder was fresh off his 714th home run, which tied him with Babe Ruth for second on the all-time list, behind Hank Aaron’s 755. In the visiting dugout was Pujols. At 26, the Cardinals’ first baseman is in his prime and entered the series with 22 homers in the season’s first 44 games, positioning him for a run at Bonds’s single-season record of 73.

Pujols clubbed his 23rd homer on Tuesday, keeping him on a 79-homer pace (though three games behind Bonds’s 2001 pace). Bonds, who went 13 days between homers 713 and 714 and appeared to wilt in the spotlight by falling into a homerless 1-for-18 slump during a week-long homestand, singled in the first two games, then sat out the third to rest his ailing knees. So much for the changing of the guard.

In one sense, that’s happened already. Last year, with Bonds limited to 14 games by multiple knee surgeries, Pujols won his first MVP award by hitting .330 with 41 homers and 117 RBI. None of those numbers rated as a career high, but the young slugger had finished no higher than second (twice) to Bonds as the latter won the previous four awards, running his record total to seven.

But the press attention still focuses on Bonds. Though he’s still 41 homers behind Aaron, passing Ruth – the outsized folk hero who singlehandedly made the home run fashionable in the early 1920s – rates as a spectacle, in part because of Bonds’s own stated desire to “wipe out” the Bambino’s feats, accomplished during an era when the game was racially segregated.

Bonds’s protracted march has given players, fans, and the press a chance to vent their frustration with a steroid-fueled era featuring juiced-up hitters producing inflated home run totals. Prior to number 713, Philadelphia fans greeted Bonds with an oversized banner: “Ruth did it on hot dogs and beer. Aaron did it with class. How did YOU do it?” In Houston after his homerless homestand, Bonds was drilled by a pitch from journeyman Russ Springer, drawing an ovation from the hometown crowd along with an ejection and subsequent four-game suspension. Meanwhile, nearly every sports section in the country finds writers taking aim at Bonds. He’s become the perfect symbol of how the steroid era has cost baseball its most hallowed records.

Pujols, by contrast, makes an appealing icon for a post-steroid era. He wants no part of the controversies surrounding Bonds, and though he’s told the press to “give the guy a break,” he’s otherwise studiously bland. “I don’t want to be the next Barry Bonds,” he’s said. “I want to be Albert Pujols and that’s it.”

Nonetheless, Pujols hasn’t escaped suspicion. From the moment he reached the majors, he carried himself with the air of a veteran star, and produced like one as well. Maybe a bit too much; critics have questioned the validity of his January 16,1980 birthday. The annals of baseball are full of falsified birthdates, particularly among Latin American-born ballplayers who lower their ages, suggesting to scouts that they have more time to reach their peaks. It would shock no one if the Dominican-born Pujols were among those ranks.

But since September 11, 2001, the U.S. Immigration Service has required real birth certificates in order to obtain work visas, resulting in dozens of ballplayers outed as being up to six years older than first believed. Pujols was not among them, however, and the intervening years have produced no evidence suggesting he should have been.

Major League Baseball’s steroid policy has enough holes that Pujols can’t escape suspicion on that front, either. Experts believe undetectable designer steroids such as the ones Bonds allegedly used are still in circulation; “the Clear” and “the Cream,” substances central to the BALCO case, are just the tip of the iceberg when it comes to flouting the rules. Moreover, no urine test exists for the naturally-occurring Human Growth Hormone, another performance enhancer which Bonds and other sluggers, such as Jason Giambi, allegedly used. Even if Pujols never fails an MLB-administered steroid test – as the Giants’ series dawned, he announced he’d passed three so far this season – he has no way to prove his innocence to a skeptic.

Unfounded suspicions aside, Pujols is perfectly poised to inherit the mantle of the game’s greatest slugger and perhaps re-legitimize the single-season home run record. Whether he can stand up to the daily scrutiny a run for 73 would generate, or whether his body – he’s been bothered by back trouble – can keep him at the pinnacle of production for the next four months, remains to be seen.

But if Pujols falls short, he’s already made a mark on baseball history. His first five seasons rank among the game’s best by nearly every advanced metric. Baseball Prospectus’s Equivalent Average measures a hitter’s total offensive value per out, allowing for cross-era comparisons by normalizing for park effects, league scoring levels, and quality of competition, and boiling the result down to a number running along the same scale as batting average. Pujols’s .340 EqA ranks sixth among an elite group.

Soon, Barry Bonds will hit that elusive 715th home run and recede into the background; in his condition, he’s got no shot at Aaron this year, and he’s waffled over the issue of whether he’ll return in 2007. The stage for Pujols will be that much clearer, and perhaps the game can return to a time when its top home run hitters aren’t tainted by suspicion.

Mr. Jaffe is a writer for Baseball Prospectus. For more state-of-the-art commentary and analysis, visit www.baseballprospectus.com.