AIM: To investigate macular microperimetry in patients with early primary open angle glaucoma (POAG) using a new custom-made pattern, and analyze the characteristics of macular sensitivity. METHODS: This case-control study included 38 patients with POAG, who were divided into pre-perimetric glaucoma (18 eyes of 18 patients), early-stage (20 eyes of 20 patients), and control (20 eyes of 20 patients) groups. All subjects underwent standard 24-2 humphrey visual field test. An MP-3 microperimeter with a new custom-made pattern (28 testing points distributed in four quadrants, covering the central 10° of the retina) was used to evaluate macular sensitivity. Ganglion cell complex (GCC) thicknesses were examined using an RS-3000 Advance OCT system. The features of structure and function were analysed per quadrant. RESULTS: The pre-perimetric glaucoma group had significantly lower inferior hemifield macular sensitivity compared to controls (P<0.05). The early-stage POAG group had significantly lower average, inferior hemifield, inferonasal, and inferotemporal mean sensitivities compared to the pre-perimetric glaucoma group (P<0.05), and lower macular sensitivity in all sectors compared to controls (P<0.05). Regarding GCC thickness, all sectors in the early-stage POAG group became thinner compared to those in controls (P<0.05); whereas all sectors in the early-stage POAG group, except the superonasal quadrant, became thinner compared to those in the pre-perimetric glaucoma group (P<0.05). Macular sensitivity and GCC thickness were significantly associated in each sector. The inferotemporal quadrant had the highest correlation coefficients (0.840). The structure-function relationship for the inferonasal and inferotemporal sectors was stronger compared to the corresponding superior sectors. CONCLUSION: Microperimetry reveals variations in macular sensitivity in patients with early glaucoma earlier than conventional perimetry, particularly in pre-perimetric glaucoma cases in which it might be undetectable by conventional methods. The new custom-made pattern may improve the accuracy of microperimetry by enhancing point arrangement and reducing fatigue effects. Macular sensitivity measured by MP-3 with this pattern shows statistically significant structural and functional associations with the thicknesses of the GCC.