Microplastic pollution is occurring in most ecosystem, yet their presence in high altitude clouds and their influence on cloud formation and climate change are poorly known. Here we analyzed microplastics in cloud water sampled at the summits of Japan mountains at 1300–3776 m altitude by attenuated total reflection imaging and micro-Fourier transform infrared spectroscopy. We observed nine microplastics including polyethylene, polypropylene, polyethylene terephthalate, polymethyl methacrylate, polyamide 6, polycarbonate, ethylene–propylene copolymer or polyethylene–polypropylene alloy, polyurethane, and epoxy resin. Microplastic were fragmented, with mean concentrations ranging from 6.7 to 13.9 pieces per liter, and with Feret diameters ranging from 7.1 to 94.6 μm. Microplastics bearing hydrophilic groups such as carbonyl and/or hydroxyl groups were abundant, suggesting that they might have acted as condensation nuclei of cloud ice and water. Overall, our finding suggest that high-altitude microplastics cloud influence cloud formation and, in turn, might modify the climate.