Introduction The PhenX Toolkit, an online resource of well-established measures of phenotypes and exposures, now has 16 new measures recommended for assessing rare genetic conditions. Materials and Methods These measures and their protocols were selected by a working group of domain experts with input from the scientific community. Results The measures cover life stages from birth through adulthood, and include clinical scales, characterization of rare genetic conditions, bioassays, and questionnaires. Most are broadly applicable to rare genetic conditions, e.g., family history, growth charts, bone age, and body proportions. Some protocols, e.g., sweat chloride test, target specific conditions. Discussion The rare genetic condition measures complement the existing measures in the PhenX Toolkit that cover anthropometrics, demographics, mental health, and reproductive history. They are directed at research pertaining to common and complex diseases. PhenX measures are publicly available and are recommended to help standardize assessments across a range of biomedical study designs. To facilitate incorporation of measures into human subjects’ research, the Toolkit offers data collection worksheets, and compatible data dictionaries. Conclusion Widespread use of standard, PhenX measures in clinical, translational and epidemiological research will enable more uniform cross-study comparisons and increase statistical power with the potential for enhancing scientific discovery.