There are seven hidden frogs in the game, one per level:
Adapt Or Perish Reach the part after losing sight of Lee for the second time during the pursuit and get to the KPA Nano-Suit soldiers fighting an alien exosuit. Go to the right and walk up the hill with a resort bar on top. Inside the bar, enter the larger of the two bathrooms. On the toilet you will see a frog frozen to a book. Upon picking up the book, Psycho will exclaim, "It's Calmon! I've found him!" Once the book is thrown or dropped it will explode.
All The Fury Once you get to the control tower, on the first floor go to the room at the north end of the building. Once you enter the room, turn left. There are three refrigerators. Open the one in the middle to find the frog.
Below The Thunder When you get off the big yellow elevator that takes you up, find the metal grate on the roof. Shoot it and jump up into the hole to enter the vents. Move through the vents and keep taking left turns until you get to a dead end. You will find a cloaked frog on a red book titled "Croaking While Cloaking".
Call Me Ishmael After you complete the objective "Join up with Sierra airstrike team", follow the roads to the bottom of the hill and go to the resort bar to the left. Continue through the resort bar and follow the path down to the shore. Jump into the ocean and swim east. On the other side of the large cliffs jutting out of the water, you will find a small island with a campsite at the far end. You will find the frog on a crate.
Frozen Paradise After reaching the mining facility, use strength mode to jump onto the roof of the largest building on the southwest corner of the facility. Once on the roof, fall off on the south wall of the building. You will land on a balcony and find the frog.
From Hell's Heart Right after you have gone through the second tunnel (including the one you started in), jump onto the train on the tracks to the right that stops at the end of the tunnel. While on the train, look right above the entrance to the tunnel to find the frog.
Shore Leave After fending off the KPA attacks against the stranded VTOL, look for a shack to the left close to the shore. Walk along the beach to find an overturned boat. Knock the boat out of the way to find the frog.