Congenital skin pits have been observed as a sporadic anatomic variant as well as in association with trauma, maternal infection, genetic syndromes, and metabolic disorders. We present a case of a neonate with paired unilateral scapular pits, which to our knowledge has not yet been reported. Although this is favored to be a benign finding in an otherwise healthy baby, we review important considerations in the clinical evaluation of a neonate with congenital skin pitting.