Organised by, among others, far right groups Ruch Narodowy and ONR, the protests saw a few thousand people chanting "The whole of Poland sings with us," "Stop the Islamisation of Europe," and anti-EU obscenities.
In the Polish capital Warsaw, nearly 5,000 people, many chanting anti-Islamic slogans, marched through the city, an AFP correspondent also said.
"Islam will be the death of Europe", one of the banners said.
Organisers claimed the demonstration drew 10,000 people but police refused to confirm the figure.
"We`re here so that the government hears our voice and abandons any plans to welcome Muslims," one of the organisers told the crowd after starting the march with prayers which identified the participants as Roman Catholics.
Another thousand or so joined a counter-demonstration in favour of welcoming refugees to Poland, a strongly Catholic EU member state which has a population of 38 million and has seen virtually no refugees arriving, despite Europe experiencing its biggest movement of people since World War II.
Around 1,500 anti-refugee protestors also rallied in the Slovak capital Bratislava, some holding up banners reading: "You`re not welcome here so go home", an AFP correspondent said.
Another said: "Multiculturalism is a utopia, don`t open the borders".
The rally was organised by the far-right "Our Slovakia" party, led by Marian Kotleba.
Unlike neighbouring Austria and Hungary, Slovakia -- a eurozone member of 5.4 million people -- has seen few refugee arrivals this summer.
Police in the Czech capital Prague said some 800 people protested against the arrival of refugees, holding up banners saying: "Send them back!" and "Protect the borders".
Demonstrators called on the Czech government to resign and for a withdrawal from the European Union which it joined in 2004.
Elsewhere another 200 people staged a counter-demonstration in support of welcoming refugees in the Czech Republic, which has a population of 10.5 million and has seen few new arrivals in recent months.
All poorer members of the EU, Hungary, Poland, Slovakia and the Czech Republic on Friday ruled out accepting refugees under a compulsory quota system outlined by the European Commission, rejecting German pleas for European solidarity in tackling the crisis.
The European Union`s 28 interior ministers are to meet on Monday to discuss a the EC plan which involves a quota system for distributing 160,000 refugees around the bloc.