The case is presented of a 3-month-old infant diagnosed with microphthalmos and orbital cysts. Magnetic Resonance Imaging revealed a bilateral microphthalmia with a moderate right cyst and a severe left cyst. Visual potential of the right eye was uncertain. Non-surgical treatment was decided. At the age of 2 years old, physical examination showed a significant decrease of the cysts and visual acuity of hand movements due to the residual vision of his right eye. Microphthalmos with orbital cyst is a rare congenital anomaly. Cysts tend to enlarge with time. At the moment, no standard protocol for the management of this pathology has been described. Unlike in our patient, visual acuity in these patients is usually of no-light perception. The observation could be an alternative in severe cases, since there is a possibility of spontaneous reduction, displacement, or regression of the cysts.