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Short-limbed short stature is a heterogeneous condition that can result from many diseases such as bone disorder, metabolic disease, and multiple malformation syndrome. We conducted a questionnaire survey of council members of the Japanese Society of Pediatric Endocrinology and doctors of affiliated hospitals in 2010 to investigate short-limbed short stature. Among 91 hospitals, responses were obtained from 61 hospitals (67% response rate). This study also examined data of 193 short-limbed short stature patients, among whom FGFR3-related chondrodysplasia such as achondroplasia (n = 109; 56.5%) was found the most frequently. Second to achondroplasia, hypochondroplasia (n = 47; 24.4%) was the most frequently observed. Along with achondroplasia and hypochondroplasia, 31 patients with disorders of 13 other kinds and six undiagnosed patients were identified. Genetic testing for hypochondroplasia was conducted for only 27.7% of all hypochondroplasia patients, although hypochondroplasia is a heterogeneous condition with many causes, only one of which is FGFR3 mutation. We conducted a genetic analysis of 25 patients who had been clinically diagnosed as having “hypochondroplasia”. In these patients, other diseases such as acromicric dysplasia, geleophysic dysplasia, and Aarskog–Scott syndrome were included in addition to FGFR3-related hypochondroplasia (n = 10). Clinical diagnosis of each disorder causing short-limbed short stature is difficult. Therefore, not only clinical diagnosis but also genetic diagnosis play an important role in the diagnosis of short-limb short stature. Diagnostic strategies must be created for each disorder.