The murine Calpain 15 (Capn15) is an intracellular cysteine protease that belongs to the non-classical Small Optic Lobe (SOL) family of calpains. SOL calpains lack the penta-EF-hand structure found in classical calpains, but have N-terminal Zinc Fingers that bind polyubiquitin and a C-terminal SOL domain with poorly characterized function.In this study, we have generated Capn15 transgenic mice and taking advantage of the lacZ reporter under the control of the Capn15 promoter, show that Capn15 is highly expressed in the developing brain and is enriched in the eyes, the superficial cortical layers, the hippocampus, and the Purkinje cells in the cerebellum in the adult. The homozygous loss of Capn15 decreases embryonic survival and weaned mice have smaller brains and weigh less than their WT littermates. MRI studies revealed specific volume losses in the superior parietal cortex and thalamus and in the CA1, CA2, dentate gyrus and stratum granulosum in the hippocampus. Most importantly, Capn15 KO mice had mild to severe eye deficits that ranged from cataracts to microphthalmia (small eye) and anophthalmia (no eye). We further identify a missense homozygous variant of CAPN15 in one patient from a UK cohort with ocular anomalies indicating a potential link between CAPN15 and microphthalmia in humans. Surprisingly, knocking-out the atypical PKC/PKMζ in Capn15 KO mice rescues the severe eye deficits in these mice suggesting that cleavage of PKCζ by Capn15 may play an important role in eye development.