Background: Alopecia areata (AA) is common during childhood and rarely reported in infants. The four reported cases of AA in infants all exhibited circumscribed patches of alopecia that appeared at birth or shortly thereafter. Objective: We report a case of alopecia areata universalis that developed after birth along with fingernail changes of shortening (onychomadesis) and onycholysis. Scalp biopsy at 2 years of age revealed rare, intermediate, terminal follicles in catagen associated with sparse peribulbar lymphocytic infiltrates. Results: This constellation of clinicopathologic features was interpreted as AA. We discuss the differential diagnosis of generalized alopecia in healthy infants, in particular, Clouston's syndrome, a hair-nail (hidrotic) ectodermal dysplasia found in this region. Genetic testing for linked polymorphisms to the Clouston gene locus were negative in this child and his parents. Conclusions: Alopecia areata should be included in the differential diagnosis of generalized alopecia presenting at or shortly after birth. For purposes of genetic counseling and prognosis, it is crucial that a correct diagnosis be made.