The first report found that in Romania the Roma minority, commonly known as gypsies, are discriminated against in all areas of life and even suffer violence at the hands of police.
The minority faces similar treatment in Lithuania but the report discovered that Jews and Chechens also experienced hostility within the community.
Last year experts from the Council of Europe's committee against racism and intolerance (ECRI) visited Romania and revealed that the discrimination was in stark contrast to new legislation designed to protect and improve the living standards of the Roma people.
The experts said that the four-year-old laws had hardly ever been enforced and that very few people, including civil servants working for the government, had heard of the country's newly-created National Anti-discrimination Council.
The ECRI had found the number of cases of discrimination had slightly decreased since its last visit in 2003 but anti-Roma articles were still common in the Romanian press.
In Lithuania the committee said anti-racism legislation designed to stamp out racist remarks and incitement to racial hatred was not being properly enforced.
Anti-Semitism also appeared to be on the increase and the ECRI urged the Lithuanian government to implement a public education program to reduce racist crimes.