The annual march also attracted a considerable number of supporters of the governing conservative Law and Justice (PiS) party to honour the reestablishment of Poland's independence in 1918.
This year's slogan was "We Want God", which 21-year-old Pawel from the southern city of Rzeszow said was "important because religion is important in our country and we don't want Islamisation, of Europe or especially Poland."
Those marching chanted "God, honour, country" and "Glory to our heroes", while a few people also shouted xenophobic lines like "Pure Poland, white Poland" and "Refugees get out".
A smaller rally of a couple thousand people earlier in the day protested what they called the "fascist" nature of the main march.
"I'm shocked that they're allowed to demonstrate on this day. It's 50 to100,000 mostly football hooligans hijacking patriotism," said 50-year-old Briton Andy Eddles, a language teacher who has been living in Poland for 27 years.
"For me it's important to support the anti-fascist coalition, and to support fellow democrats, who are under pressure in Poland today," he told AFP.
Main march participant Kamil Staszalek however warned against making generalisations and said he was marching to "honour the memory of those who fought for Poland's freedom".
"I for one don't identify with fascists. The same goes for other people - and there are families with children here too," said the 30-year-old Warsaw office-worker.
"I'd say some people here do have extreme views, maybe even 30 percent of those marching, but 70 percent are simply walking peacefully, without shouting any fascist slogans," he told AFP.
No monopoly on patriotism
Polish President Andrzej Duda hosted an official ceremony to mark 99 years since Poland regained independence after being wiped off the map for 123 years in a three-way carve-up between Tsarist Russia, Prussia and the Austro-Hungarian Empire.
Duda invites all living former Polish presidents and premiers to attend each year, and Saturday marked the first time since the PiS party came to power in 2015 that EU President Donald Tusk - a former Polish premier and PiS rival - decided to attend.
"Independence Day has always been and will continue to be a celebration of all Poles and not just one party. No politician in Poland has ever had nor will ever have a monopoly on patriotism," Tusk told reporters upon arriving at Warsaw's Chopin airport.
Tusk's appearance comes at a time when Warsaw has been increasingly at odds with Brussels because of the PiS government's controversial court reforms, large-scale logging in a primeval forest and refusal to welcome migrants.
Relations between PiS and Tusk have been so tense that Poland was the only country to vote against his reelection as EU president in March.
Warsaw business-owner Wojciech Krol, who attended the anti-fascist rally with a huge Polish flag, said he was a Tusk opponent for a long time but is now happy with his work in the European Union and glad that he returned to Poland on Saturday.
"I'm really happy he came. What we want most here is as much Europe as possible. Because right now it is only global pressure, and specifically EU pressure, that has stopped us all from being arrested, beaten, harassed, and so on," the 55-year-old government critic told AFP.
