Current regulations require that the assessment of protein quality in infant formula be determined using the protein efficiency ratio (PER) rat bioassay where the growth of rats fed a test protein is compared with the growth of rats fed casein. This review cites authoritative body opinions that the PER is not a preferred method for scoring protein quality, particularly as applied to the infant formula. Methodological recommendations specified by FDA and recent guidance propose to control nonprotein dietary variables in the PER. In contrast, the essential amino acid pattern of human milk has been adopted internationally as the standard for protein quality in infant formula. Because casein, the control protein in the PER fails to meet the standard of human milk essential amino acids, the PER based on casein can generate a false assurance of the quality of protein in an infant formula. FDA should revise the method of demonstrating the quality factor for the biological quality of protein to the essential amino acid pattern of human milk, which would be simpler, conform to international standards, and should be considered by FDA under a new statute. Alternate methods of determination of protein quality can be used selectively when there are questions about the digestibility of new protein sources or the effects of manufacturing processes.