Diurnal rainfall variations over three subdomains with distinct annual rainfall cycles within Indonesia have been analyzed using Tropical Rainfall Measuring Mission datasets (3B42) for the period of 2000 to 2009. Empirical Orthogonal Functions (EOF) analysis was used to compare spatial-temporal variability among three selected areas (A, B and C). The EOF analysis revealed that the three regions showed dominant diurnal cycles of rainfall. The diurnal cycles of the three regions were marked by different amplitudes and phases, particularly over land and oceanic regimes. Region A exhibited an afternoon peak over land and a morning peak over ocean. Region B showed an evening peak over the land and a morning peak over the ocean.While Region C exhibited an afternoon peak over the land and an early morning to noon peak over the ocean. Over coastal areas, the same midnight peak was observed for the three regions. The result of this study provides relevant information to understand the effects of island size and land- sea formation on the characteristics of the diurnal rainfall variation, particularly over the Indonesian Maritime Continent