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Microspherophakia is a developmental lens anomaly characterized by increased anteroposterior diameter and reduced equatorial diameter, which predisposes to secondary glaucoma. A 12-year-old boy presented with diminution of vision. Slit-lamp examination showed anteriorly dislocated crystalline lens. Blood analysis revealed elevated homocysteine levels. Genetic analysis showed cystathionine beta-synthase gene mutation, thus confirming the diagnosis of homocystinuria. To prevent secondary glaucoma, the patient was taken up for surgical intervention. This report highlights a case of homocystinuria with microspherophakia diagnosed with the help of genetic testing.