Line the baking pan with foil. Set aside 1-1/2 cups pretzels for topping.
Grind the rest of the pretzels in a food processor until fine crumbs form.
In a large bowl, mix butter, peanut butter, confectioners' sugar, and pretzel crumbs. Press the peanut butter mixture into the prepared pan.
In a microwave, melt chocolate chips and shortening; stir until smooth. Spread over peanut butter layer.
Break reserved pretzels and sprinkle over top; press down gently. Refrigerate, covered, until set (about 1 hour). Lift with the foil to remove from pan. Cut into 48 bars.