A method and system for partial connection of iterations during loop unrolling during compilation of a program by a compiler. Unrolled loop iterations of a loop in the program are selectively connected during loop unrolling during the compilation, including redirecting, to the head of the loop, undesirable edges of a control flow from one iteration to a next iteration of the loop. Merges on a path of hot code are removed to increase a scope for optimization of the program. The head of the loop and a start of a replicated loop body of the loop are equivalent points of the control flow.