Karim Benzema, Sergio Ramos and Marco Asensio were on target as Madrid marched into the last eight.
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Zinédine Zidane's side produced a clinical performance to complete a 4-1 aggregate success against Atalanta in this round of 16 tie.
Match in brief
Atalanta started proceedings at a furious pace and should have taken the lead inside three minutes only for Robin Gosens to shoot tamely at Thibaut Courtois from Luis Muriel's cross. The visitors were made to rue that miss when Karim Benzema broke the deadlock, sweeping in Luka Modrić's pass after a poor clearance by Marco Sportiello.
Madrid asserted their dominance after the interval with Vinícius Júnior poking wide after a scintillating run then being felled in the area by Rafael Tolói, Sergio Ramos rifling in the resulting penalty. Muriel did reduce arrears with a wonderful free-kick but Madrid quickly completed the scoring as Marco Asensio drilled in their third on the counterattack.
Player of the Match: Luka Modrić (Real Madrid)
"Thanks to his balance in attack and defence, organisation of the game throughout and great assist for the first goal – the best player on the pitch for the whole game."
Ginés Meléndez, UEFA Technical Observer
Joe Walker, Real Madrid reporter
A new-look system but a familiar result for Madrid in Europe. Truth be told, for all Atalanta's huffing and puffing they rarely threatened to blow the house down, and it was Madrid's old guard who did the damage. Nobody will fancy drawing Zidane's side on Friday.
Vieri Capretta, Atalanta reporter
A great start, and then a beautiful goal when it was too late. In the middle, Atalanta simply struggled against a technically better side. Sportiello's mistakes at the back made it even tougher, and not taking chances up front meant the tie was never really in doubt. Both tactically and technically, Gian Piero Gasperini's men simply weren't on their usual level, and against such a strong team you need to be perfect.
Sergio Ramos, Real Madrid captain: "Our aim was to get through and we achieved that with a great result. We could have scored more and we're happy with how we played. You adapt your approach to your opponent. We didn't know how they were going to press but we quickly took control thanks to our three-at-the-back set-up. We knew that with their speed they could be dangerous, but it went well and they didn't really threaten us."
Luka Modrić, Real Madrid midfielder: "We had to match them physically and with the ball, and we did that. We're really happy. The first goal was really important to get. The boss asked us to press high and that's what we did, and it gave us confidence."
Thibaut Courtois, Real Madrid goalkeeper: "I'm happy with the performance and getting through. We put in a lot of effort and could've scored more. Atalanta, who are a side who score a lot of goals in Italy, only got one against us and that was from a set piece. We were great defensively. We know how to press and when to take a step back."
Duván Zapata, Atalanta striker: "We're disappointed as we wanted to progress. We struggled to play our football tonight, sadly it went like this. We started well, pressing high, but then our mistakes made it harder for us."
• Benzema is the fifth player to score 70 UEFA Champions League goals after Lionel Messi, Robert Lewandowski, Cristiano Ronaldo and Raúl González.
• Madrid have scored in their last 22 UEFA Champions League knockout matches – the last time they drew a blank was against Manchester City in their 2015/16 semi-final first leg.
• Madrid have scored two or more goals in seven of their last eight UEFA Champions League home games.
• The Merengues have won 12 of their last 13 matches against Italian clubs in this competition.
• Atalanta have not scored a first-half goal in their last seven UEFA Champions League games.
Real Madrid: Courtois; Nacho, Varane, Ramos (Éder Militão 64), Mendy; Kroos, Modrić, Valverde (Asensio 82); Vázquez, Benzema, Vinícius (Rodrygo 69)
Atalanta: Sportiello; Tolói (Palomino 61), Romero, Djimsiti; Mæhle, De Roon, Pessina (Caldara 84), Gosens (Iličić 57); Pašalić (Zapata 46), Malinovskyi; Muriel (Miranchuk 84)
The quarter-final and semi-final draws will be streamed live on UEFA.com from midday CET on Friday 19 March. There are no seedings or country protection.