The evolution of the morphology and composition of the single-crystal silicon surface irradiated by infrared and visible nanosecond laser pulses is investigated as a function of processing parameters (laser fluence, irradiation spot size, the number of pulses, background gas pressure and composition). Two types of periodic surface microstructures are obtained with IR (1064 nm) laser pulses in a narrow fluence range of 3–6 J/cm2. At a relatively low number of laser pulses applied, a grid of cleavage cracks is produced within the irradiation spot along the crystal orientation. With further Si irradiation, periodic microhillocks are formed in the nodes of the crack grid. Silicon surface with such microhillocks exhibits superhydrophilic properties which are retained during prolonged storage in air. The cracks are produced in any environment (including vacuum) but the microhillocks are observed only in the presence of oxygen. No periodic structures were observed with visible (532 nm) laser pulses. Mechanisms of nanosecond laser-induced periodic microstructure formation on silicon are discussed.