Both countries take it as a deliberate diplomatic snub. Polish President Aleksander Kwasniewski said it was no accident. The Lithuanian president, Valdas Adamkus, asked members of his government not to attend the celebrations.
Being not invited looks strange as the two countries have much longer history with the region of which Russia took control only after the World War II.
However, analysts are only guessing why Lithuanian and Poland are not welcomed.
Vytautas Radzvilas, an analyst in the Lithuanian Institute of International Affairs in Vilnius, says Lithuania did a lot to help the region to adopt its new geopolitical and economic situation. He says Russia might be saying it doesn't need this kind of help.
"Getting no invitation to the celebrations is also understood as devaluation of these [Lithuanian efforts]," Radzvilas said.
Radzvilas says some Lithuanian politicians guess the Kremlin had decided to take revenge against the Lithuanian president who refused to attend the World War II anniversary celebrations held in the beginning of May in Moscow. However, Radzvilas says Kwasniewski attended the Moscow celebrations and hasn't got an invitation, either.
Kirill Koktysh, an analyst with the Moscow Institute of International Relations, says Lithuanian refusal to go to the Moscow celebrations has poisoned Russian-Lithuanian relations only for a short time. He says that at present neither Russian relations with Poland nor with Lithuania are bad.
"We can only guess [why they were not invited]. On one hand, [Russian] relations with Lithuania and Poland are not in the best shape but, on the other hand, they are not very bad," Koktysh said.
He says there might be different reasons for this Russian decision. Moscow is unhappy that Lithuania seeks compensation for the years of Soviet occupation. Moscow might be also unhappy for the Lithuanian role in encouraging democracy in Belarus.
Koktysh also says Russian relations with Poland have deteriorated during the Orange Revolution in Ukraine, when Poland supported President Viktor Yushchenko.
"Relations with Poland have a little bit deteriorated during the Orange Revolution in Kyiv, but after that there were no incidents. Recently, Poland did not make any anti-Russian declarations," Koktysh said.
Koktysh said there is no doubt that the Kremlin is sending diplomatic signals to the two countries. The problem is that the message remains a secret.
Russian President Putin's senior aide Sergei Yastrzhembskii said the Kremlin is "puzzled by speculative publications in the media of some Kaliningrad's neighbors and attempts to dictate to Russia their vision of what the celebrations should look like."
Koktysh said, with oil prices on the rise, Russia continues to be vital to German and French economies.
Moscow also wants the EU to issue special rules to allow Russian cargo and passengers to transit EU member Lithuania to reach Russia. The EU has so far not agreed to the idea.
Yastrzhembskii said the leaders were also set to discuss a list of traditional topics, including Iran's nuclear program, the situation in Iraq, the Middle East, and moves to curb proliferation of weapons of mass destruction.