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Abstract Background PNPLA2 gene mutations cause neutral lipid storage disease with myopathy (NLSD-M) or cardiomyopathies. The clinical phenotype, blood test results, imaging examination and gene analysis can be used to improve the understanding of NLSD-M, reduce the misdiagnosis rate and prevent physical disability and even premature death. Case presentation We report a Chinese child with NLSD-M presenting with marked asymmetric skeletal myopathy and hypertrophic cardiomyopathy. Blood biochemical tests revealed increased creatine kinase levels, and echocardiography revealed a diffuse and thick left ventricular wall. Gene analysis revealed a homozygous mutation c.155C > G (p.Thr52Arg) in PNPLA2. Conclusions An understanding of the characteristic features is essential for the early diagnosis of NLSD-M. Our data expand the allelic spectrum of PNPLA2 mutations, providing further evidence for genetic and clinical NLSD-M heterogeneity in younger individuals.