We present the first report of a rare form of lipoatrophic diabetes mellitus in a child with partial autoimmune lipodystrophy combined with systemic scleroderma and phenylketonuria. We describe the features of clinical manifestations, diagnosis, and therapy. To exclude the monogenic form of lipodystrophy, we performed a molecular genetic analysis of genes ZMPSTE24, LMNA, BSCL2, PLIN1, PTRF, LMNB2, POLD1, AKT2, CIDEC, PIK3CA, PPARG, PSMB8, CAV1, PPP1R3A, and AGPAT2 that are responsible for the development of lipodystrophy and insulin resistance. No mutations were found. The presence of systemic scleroderma of autoimmune genesis enabled the diagnosis of autoimmune lipodystrophy. Treatment of insulin-resistant diabetes mellitus in lipodystrophy is a challenge: biguanide therapy is dangerous due to impairment of liver functions, and insulin therapy is not effective enough; administration of high doses is required. The presence of phenylketonuria further complicates compliance with the dietary regimen. The combination of three rare diseases ― lipoatrophic diabetes, phenylketonuria, and systemic scleroderma ― in one patient has not been found in the available literature.