A breathing system in a combustion engine includes an air cleaner (3) for purifying air to be supplied to the engine. The air cleaner (3) includes a cleaner casing (30) having a blow-by gas inlet port (33) and an intake air discharge port (34). The breathing system also includes a breather passage (8) having first and second breather passage portions. The first breather passage portion is fluidly connected with the inlet port (33) for communicating a crank chamber (1a) to a portion of an interior of the air cleaner (3) downstream of the cleaner element (50). The second breather passage portion fluidly connects the blow-by gas inlet port (33) and the intake air discharge port (34) and has a drain hole (95) for draining into the cleaner casing (30) a water component, separated from a blow-by gas (G) flowing through the breather passage (8).