The anti-immigration Alternative for Germany party has polled strongly in both Brandenburg and Saxony states, part of its eastern electoral heartland.
Aside from railing against Islam and asylum- seekers, the AfD has capitalised on resentment about a lingering east-west wealth gap since the 1989 fall of the Berlin Wall.
“Let's complete the Wende” (turnaround), it has vowed, referring to the peaceful revolution that ended the Soviet-allied one party state and brought national reunification in 1990.
The AfD has long co-opted the former pro-democracy chant “We are the people” and turned it against what it labels the “Merkel regime”.
Eastern Germany is home to several of the AfD's most extremist leaders, among them Bjoern Hoecke, who has labelled Berlin's Holocaust memorial a “monument of shame”.
His close ally, former paratrooper Andreas Kalbitz, 46, who has had deep ties to right-wing extremist groups, is the top candidate in Brandenburg.
Der Spiegel weekly has reported that in 2007 Kalbitz joined known German neo-Nazis on a visit to Athens that came to police attention because of a swastika flag flown from a hotel balcony.
Kalbitz confirmed to the magazine that he joined the trip but insisted that the event “was not conducive to arousing my further interest or approval”.
Dietmar Woidke (SPD), Minister President of Brandenburg, voting on Sunday. Photo: Michael Kappeler/dpa
In Brandenburg, which surrounds Berlin, the AfD has been polling neck and neck with the governing Social Democratic Party (SPD), both at just over 20 percent.
In Saxony, the state where the extremist anti-Islam Pegida street movement was born, the AfD has slipped back somewhat behind Merkel's centre-right Christian Democrats (CDU).
But even if the AfD emerges as the strongest party in either state, the other major parties are expected to shut it out from governing by forming coalitions to achieve majorities.
Political scientist Wolfgang Schroeder of Kassel University said that election gains could therefore spell a “successful failure” for the AfD.
“Although it has a high voter turnout and has contributed to shifting the political discourse to the right, it has little real political effect,” he said.
A third election will be held on October 27 in the eastern state of Thuringia.
The AfD, formed six years ago as a eurosceptic group, now focuses mainly on fear and anger over Germany's mass migrant influx since 2015.
Merkel, who also grew up in the east, has avoided campaigning ahead of Sunday's polls in the region, where she has in the past faced harsh abuse.
For Merkel, an election debacle for either her CDU or junior coalition partner the SPD would pose another threat to their uneasy coalition.
The veteran leader has already pledged to step down when her current term ends in 2021, but regional election upsets could speed up her government's demise.
Poor results for the SPD, already demoralised by a string of election defeats, would boost internal critics who want the party to leave Merkel's government quickly.